PDB Short entry for 2GZD HEADER PROTEIN TRANSPORT 11-MAY-06 2GZD TITLE CRYSTAL STRUCTURE OF RAB11 IN COMPLEX WITH RAB11-FIP2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-11A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: G PROTEIN DOMAIN; COMPND 5 SYNONYM: RAB-11, YL8; COMPND 6 EC: 3.6.5.2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RAB11 FAMILY-INTERACTING PROTEIN 2; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: RAB11-FIP2 RAB-BINDING DOMAIN; COMPND 13 SYNONYM: RAB11-FIP2, NRIP11; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAB11A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PMAL-C2X KEYWDS G PROTEIN FOLDS, A-HELICAL COILED COIL, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.R.KHAN REVDAT 5 03-APR-24 2GZD 1 REMARK REVDAT 4 20-OCT-21 2GZD 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2GZD 1 VERSN REVDAT 2 29-AUG-06 2GZD 1 JRNL REVDAT 1 15-AUG-06 2GZD 0 JRNL AUTH W.N.JAGOE,A.J.LINDSAY,R.J.READ,A.J.MCCOY,M.W.MCCAFFREY, JRNL AUTH 2 A.R.KHAN JRNL TITL CRYSTAL STRUCTURE OF RAB11 IN COMPLEX WITH RAB11 FAMILY JRNL TITL 2 INTERACTING PROTEIN 2. JRNL REF STRUCTURE V. 14 1273 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16905101 JRNL DOI 10.1016/J.STR.2006.06.010 REMARK 2 REMARK 2 RESOLUTION. 2.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 24064 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1290 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 50.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1717 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 1290 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3258 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.45000 REMARK 3 B22 (A**2) : 0.58000 REMARK 3 B33 (A**2) : 2.87000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.321 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.261 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.192 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.166 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.876 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3384 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4595 ; 1.974 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 402 ; 9.512 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 163 ;34.282 ;23.374 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 587 ;19.594 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;23.053 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 524 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2509 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1560 ; 0.240 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2283 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 175 ; 0.191 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.049 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 13 ; 0.145 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.313 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2093 ; 1.154 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3253 ; 1.857 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1514 ; 2.488 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1342 ; 3.732 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 7 A 173 4 REMARK 3 1 B 7 B 173 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1328 ; 0.43 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1328 ; 0.89 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : C D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 C 473 C 500 4 REMARK 3 1 D 473 D 500 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 C (A): 239 ; 0.35 ; 0.50 REMARK 3 MEDIUM THERMAL 2 C (A**2): 239 ; 0.73 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2GZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97865 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24064 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.42100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: RAB11 IN COMPLEX WITH RAB11-FIP IN THE TRIGONAL REMARK 200 SPACE GROUP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM PHOSPHATE BUFFER, BETWEEN 0.1 REMARK 280 AND 0.5 M CONCENTRATION, VAPOR DIFFUSION, TEMPERATURE 298K, PH 5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 32.18200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.54950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.57450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.54950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.18200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.57450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL UNIT CONSISTS OF TWO MOLECULES OF RAB11 AND REMARK 300 TWO MOLECULES OF RAB11-FIP2, WITH THE RAB11-FIP2 MOLECULE FORMING A REMARK 300 CENTRAL PARALLEL COILED COIL NEARLY COINCIDENT WITH THE REMARK 300 CRYSTALLOGRAPHIC C-AXIS. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 THR A 3 REMARK 465 ARG A 4 REMARK 465 ASP A 5 REMARK 465 ASP A 6 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 THR B 3 REMARK 465 ARG B 4 REMARK 465 ASP B 5 REMARK 465 ASP B 6 REMARK 465 GLY C 406 REMARK 465 ALA C 407 REMARK 465 MET C 408 REMARK 465 ALA C 409 REMARK 465 ALA C 410 REMARK 465 LYS C 411 REMARK 465 PHE C 412 REMARK 465 ARG C 413 REMARK 465 ALA C 414 REMARK 465 SER C 415 REMARK 465 ASN C 416 REMARK 465 ILE C 417 REMARK 465 MET C 418 REMARK 465 PRO C 419 REMARK 465 SER C 420 REMARK 465 SER C 421 REMARK 465 SER C 422 REMARK 465 PHE C 423 REMARK 465 HIS C 424 REMARK 465 MET C 425 REMARK 465 SER C 426 REMARK 465 PRO C 427 REMARK 465 THR C 428 REMARK 465 SER C 429 REMARK 465 ASN C 430 REMARK 465 GLU C 431 REMARK 465 ASP C 432 REMARK 465 LEU C 433 REMARK 465 ARG C 434 REMARK 465 LYS C 435 REMARK 465 ILE C 436 REMARK 465 PRO C 437 REMARK 465 ASP C 438 REMARK 465 SER C 439 REMARK 465 ASN C 440 REMARK 465 PRO C 441 REMARK 465 PHE C 442 REMARK 465 ASP C 443 REMARK 465 ALA C 444 REMARK 465 THR C 445 REMARK 465 ALA C 446 REMARK 465 GLY C 447 REMARK 465 TYR C 448 REMARK 465 ARG C 449 REMARK 465 SER C 450 REMARK 465 LEU C 451 REMARK 465 THR C 452 REMARK 465 TYR C 453 REMARK 465 GLU C 454 REMARK 465 GLU C 455 REMARK 465 VAL C 456 REMARK 465 LEU C 457 REMARK 465 GLN C 458 REMARK 465 GLU C 459 REMARK 465 LEU C 460 REMARK 465 VAL C 461 REMARK 465 LYS C 462 REMARK 465 HIS C 463 REMARK 465 LYS C 464 REMARK 465 GLU C 465 REMARK 465 LEU C 466 REMARK 465 LEU C 467 REMARK 465 SER C 503 REMARK 465 ARG C 504 REMARK 465 LYS C 505 REMARK 465 ALA C 506 REMARK 465 GLY C 507 REMARK 465 LYS C 508 REMARK 465 PHE C 509 REMARK 465 SER C 510 REMARK 465 ASN C 511 REMARK 465 SER C 512 REMARK 465 GLY D 406 REMARK 465 ALA D 407 REMARK 465 MET D 408 REMARK 465 ALA D 409 REMARK 465 ALA D 410 REMARK 465 LYS D 411 REMARK 465 PHE D 412 REMARK 465 ARG D 413 REMARK 465 ALA D 414 REMARK 465 SER D 415 REMARK 465 ASN D 416 REMARK 465 ILE D 417 REMARK 465 MET D 418 REMARK 465 PRO D 419 REMARK 465 SER D 420 REMARK 465 SER D 421 REMARK 465 SER D 422 REMARK 465 PHE D 423 REMARK 465 HIS D 424 REMARK 465 MET D 425 REMARK 465 SER D 426 REMARK 465 PRO D 427 REMARK 465 THR D 428 REMARK 465 SER D 429 REMARK 465 ASN D 430 REMARK 465 GLU D 431 REMARK 465 ASP D 432 REMARK 465 LEU D 433 REMARK 465 ARG D 434 REMARK 465 LYS D 435 REMARK 465 ILE D 436 REMARK 465 PRO D 437 REMARK 465 ASP D 438 REMARK 465 SER D 439 REMARK 465 ASN D 440 REMARK 465 PRO D 441 REMARK 465 PHE D 442 REMARK 465 ASP D 443 REMARK 465 ALA D 444 REMARK 465 THR D 445 REMARK 465 ALA D 446 REMARK 465 GLY D 447 REMARK 465 TYR D 448 REMARK 465 ARG D 449 REMARK 465 SER D 450 REMARK 465 LEU D 451 REMARK 465 THR D 452 REMARK 465 TYR D 453 REMARK 465 GLU D 454 REMARK 465 GLU D 455 REMARK 465 VAL D 456 REMARK 465 LEU D 457 REMARK 465 GLN D 458 REMARK 465 GLU D 459 REMARK 465 LEU D 460 REMARK 465 VAL D 461 REMARK 465 LYS D 462 REMARK 465 HIS D 463 REMARK 465 LYS D 464 REMARK 465 GLU D 465 REMARK 465 LEU D 466 REMARK 465 LEU D 467 REMARK 465 SER D 503 REMARK 465 ARG D 504 REMARK 465 LYS D 505 REMARK 465 ALA D 506 REMARK 465 GLY D 507 REMARK 465 LYS D 508 REMARK 465 PHE D 509 REMARK 465 SER D 510 REMARK 465 ASN D 511 REMARK 465 SER D 512 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ARG D 497 O PRO D 499 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP B 157 CB - CA - C ANGL. DEV. = -13.6 DEGREES REMARK 500 PRO C 502 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 39 31.74 -95.04 REMARK 500 ASP A 56 -145.47 51.82 REMARK 500 LEU A 128 56.20 -90.52 REMARK 500 SER A 158 -4.51 89.11 REMARK 500 ASN A 160 -2.54 71.02 REMARK 500 ASP B 19 157.11 -42.90 REMARK 500 ASP B 56 -132.00 66.40 REMARK 500 LEU B 70 51.24 -113.37 REMARK 500 GLU B 71 68.08 11.65 REMARK 500 TYR B 73 104.04 -47.27 REMARK 500 SER B 115 -12.47 -45.76 REMARK 500 LYS B 125 42.13 74.24 REMARK 500 LEU B 128 48.82 -86.49 REMARK 500 SER B 158 -6.97 82.21 REMARK 500 PRO D 499 -159.95 -76.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 57 LYS A 58 -147.21 REMARK 500 ALA B 68 GLY B 69 112.34 REMARK 500 GLU B 71 ARG B 72 124.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 950 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 25 OG REMARK 620 2 THR A 43 OG1 87.1 REMARK 620 3 GTP A 900 O2G 154.5 91.4 REMARK 620 4 GTP A 900 O2B 77.5 152.9 93.1 REMARK 620 5 HOH A 951 O 74.8 84.5 79.7 70.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 950 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 25 OG REMARK 620 2 THR B 43 OG1 76.6 REMARK 620 3 GTP B 900 O2G 143.4 86.6 REMARK 620 4 GTP B 900 O2B 92.6 150.3 86.2 REMARK 620 5 HOH B 986 O 73.1 72.8 70.9 77.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 950 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 950 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP B 900 DBREF 2GZD A 2 173 UNP P62491 RB11A_HUMAN 1 172 DBREF 2GZD B 2 173 UNP P62491 RB11A_HUMAN 1 172 DBREF 2GZD C 410 512 UNP Q7L804 RFIP2_HUMAN 410 512 DBREF 2GZD D 410 512 UNP Q7L804 RFIP2_HUMAN 410 512 SEQADV 2GZD MET A 1 UNP P62491 CLONING ARTIFACT SEQADV 2GZD LEU A 70 UNP P62491 GLN 69 ENGINEERED MUTATION SEQADV 2GZD MSE A 120 UNP P62491 MET 119 MODIFIED RESIDUE SEQADV 2GZD MET B 1 UNP P62491 CLONING ARTIFACT SEQADV 2GZD LEU B 70 UNP P62491 GLN 69 ENGINEERED MUTATION SEQADV 2GZD MSE B 120 UNP P62491 MET 119 MODIFIED RESIDUE SEQADV 2GZD GLY C 406 UNP Q7L804 CLONING ARTIFACT SEQADV 2GZD ALA C 407 UNP Q7L804 CLONING ARTIFACT SEQADV 2GZD MET C 408 UNP Q7L804 CLONING ARTIFACT SEQADV 2GZD ALA C 409 UNP Q7L804 CLONING ARTIFACT SEQADV 2GZD MSE C 489 UNP Q7L804 MET 489 MODIFIED RESIDUE SEQADV 2GZD GLY D 406 UNP Q7L804 CLONING ARTIFACT SEQADV 2GZD ALA D 407 UNP Q7L804 CLONING ARTIFACT SEQADV 2GZD MET D 408 UNP Q7L804 CLONING ARTIFACT SEQADV 2GZD ALA D 409 UNP Q7L804 CLONING ARTIFACT SEQADV 2GZD MSE D 489 UNP Q7L804 MET 489 MODIFIED RESIDUE SEQRES 1 A 173 MET GLY THR ARG ASP ASP GLU TYR ASP TYR LEU PHE LYS SEQRES 2 A 173 VAL VAL LEU ILE GLY ASP SER GLY VAL GLY LYS SER ASN SEQRES 3 A 173 LEU LEU SER ARG PHE THR ARG ASN GLU PHE ASN LEU GLU SEQRES 4 A 173 SER LYS SER THR ILE GLY VAL GLU PHE ALA THR ARG SER SEQRES 5 A 173 ILE GLN VAL ASP GLY LYS THR ILE LYS ALA GLN ILE TRP SEQRES 6 A 173 ASP THR ALA GLY LEU GLU ARG TYR ARG ALA ILE THR SER SEQRES 7 A 173 ALA TYR TYR ARG GLY ALA VAL GLY ALA LEU LEU VAL TYR SEQRES 8 A 173 ASP ILE ALA LYS HIS LEU THR TYR GLU ASN VAL GLU ARG SEQRES 9 A 173 TRP LEU LYS GLU LEU ARG ASP HIS ALA ASP SER ASN ILE SEQRES 10 A 173 VAL ILE MSE LEU VAL GLY ASN LYS SER ASP LEU ARG HIS SEQRES 11 A 173 LEU ARG ALA VAL PRO THR ASP GLU ALA ARG ALA PHE ALA SEQRES 12 A 173 GLU LYS ASN GLY LEU SER PHE ILE GLU THR SER ALA LEU SEQRES 13 A 173 ASP SER THR ASN VAL GLU ALA ALA PHE GLN THR ILE LEU SEQRES 14 A 173 THR GLU ILE TYR SEQRES 1 B 173 MET GLY THR ARG ASP ASP GLU TYR ASP TYR LEU PHE LYS SEQRES 2 B 173 VAL VAL LEU ILE GLY ASP SER GLY VAL GLY LYS SER ASN SEQRES 3 B 173 LEU LEU SER ARG PHE THR ARG ASN GLU PHE ASN LEU GLU SEQRES 4 B 173 SER LYS SER THR ILE GLY VAL GLU PHE ALA THR ARG SER SEQRES 5 B 173 ILE GLN VAL ASP GLY LYS THR ILE LYS ALA GLN ILE TRP SEQRES 6 B 173 ASP THR ALA GLY LEU GLU ARG TYR ARG ALA ILE THR SER SEQRES 7 B 173 ALA TYR TYR ARG GLY ALA VAL GLY ALA LEU LEU VAL TYR SEQRES 8 B 173 ASP ILE ALA LYS HIS LEU THR TYR GLU ASN VAL GLU ARG SEQRES 9 B 173 TRP LEU LYS GLU LEU ARG ASP HIS ALA ASP SER ASN ILE SEQRES 10 B 173 VAL ILE MSE LEU VAL GLY ASN LYS SER ASP LEU ARG HIS SEQRES 11 B 173 LEU ARG ALA VAL PRO THR ASP GLU ALA ARG ALA PHE ALA SEQRES 12 B 173 GLU LYS ASN GLY LEU SER PHE ILE GLU THR SER ALA LEU SEQRES 13 B 173 ASP SER THR ASN VAL GLU ALA ALA PHE GLN THR ILE LEU SEQRES 14 B 173 THR GLU ILE TYR SEQRES 1 C 107 GLY ALA MET ALA ALA LYS PHE ARG ALA SER ASN ILE MET SEQRES 2 C 107 PRO SER SER SER PHE HIS MET SER PRO THR SER ASN GLU SEQRES 3 C 107 ASP LEU ARG LYS ILE PRO ASP SER ASN PRO PHE ASP ALA SEQRES 4 C 107 THR ALA GLY TYR ARG SER LEU THR TYR GLU GLU VAL LEU SEQRES 5 C 107 GLN GLU LEU VAL LYS HIS LYS GLU LEU LEU ARG ARG LYS SEQRES 6 C 107 ASP THR HIS ILE ARG GLU LEU GLU ASP TYR ILE ASP ASN SEQRES 7 C 107 LEU LEU VAL ARG VAL MSE GLU GLU THR PRO SER ILE LEU SEQRES 8 C 107 ARG VAL PRO TYR GLU PRO SER ARG LYS ALA GLY LYS PHE SEQRES 9 C 107 SER ASN SER SEQRES 1 D 107 GLY ALA MET ALA ALA LYS PHE ARG ALA SER ASN ILE MET SEQRES 2 D 107 PRO SER SER SER PHE HIS MET SER PRO THR SER ASN GLU SEQRES 3 D 107 ASP LEU ARG LYS ILE PRO ASP SER ASN PRO PHE ASP ALA SEQRES 4 D 107 THR ALA GLY TYR ARG SER LEU THR TYR GLU GLU VAL LEU SEQRES 5 D 107 GLN GLU LEU VAL LYS HIS LYS GLU LEU LEU ARG ARG LYS SEQRES 6 D 107 ASP THR HIS ILE ARG GLU LEU GLU ASP TYR ILE ASP ASN SEQRES 7 D 107 LEU LEU VAL ARG VAL MSE GLU GLU THR PRO SER ILE LEU SEQRES 8 D 107 ARG VAL PRO TYR GLU PRO SER ARG LYS ALA GLY LYS PHE SEQRES 9 D 107 SER ASN SER MODRES 2GZD MSE A 120 MET SELENOMETHIONINE MODRES 2GZD MSE B 120 MET SELENOMETHIONINE MODRES 2GZD MSE C 489 MET SELENOMETHIONINE MODRES 2GZD MSE D 489 MET SELENOMETHIONINE HET MSE A 120 8 HET MSE B 120 8 HET MSE C 489 8 HET MSE D 489 8 HET MG A 950 1 HET GTP A 900 32 HET MG B 950 1 HET GTP B 900 32 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 5 MG 2(MG 2+) FORMUL 6 GTP 2(C10 H16 N5 O14 P3) FORMUL 9 HOH *78(H2 O) HELIX 1 1 GLY A 23 ASN A 34 1 12 HELIX 2 2 ILE A 76 ARG A 82 1 7 HELIX 3 3 LYS A 95 ASN A 101 1 7 HELIX 4 4 ASN A 101 ALA A 113 1 13 HELIX 5 5 LEU A 128 ARG A 132 5 5 HELIX 6 6 PRO A 135 ASN A 146 1 12 HELIX 7 7 ASN A 160 TYR A 173 1 14 HELIX 8 8 GLY B 23 ASN B 34 1 12 HELIX 9 9 ILE B 76 ARG B 82 1 7 HELIX 10 10 LYS B 95 ASN B 101 1 7 HELIX 11 11 ASN B 101 ALA B 113 1 13 HELIX 12 12 PRO B 135 ASN B 146 1 12 HELIX 13 13 ASN B 160 TYR B 173 1 14 HELIX 14 14 ARG C 469 THR C 492 1 24 HELIX 15 15 PRO C 493 ARG C 497 5 5 HELIX 16 16 ARG D 468 THR D 492 1 25 HELIX 17 17 PRO D 493 ARG D 497 5 5 SHEET 1 A 6 VAL A 46 VAL A 55 0 SHEET 2 A 6 LYS A 58 THR A 67 -1 O ILE A 60 N ILE A 53 SHEET 3 A 6 TYR A 10 ILE A 17 1 N PHE A 12 O GLN A 63 SHEET 4 A 6 GLY A 86 ASP A 92 1 O LEU A 88 N ILE A 17 SHEET 5 A 6 VAL A 118 ASN A 124 1 O ASN A 124 N TYR A 91 SHEET 6 A 6 SER A 149 GLU A 152 1 O SER A 149 N LEU A 121 SHEET 1 B 6 VAL B 46 VAL B 55 0 SHEET 2 B 6 LYS B 58 THR B 67 -1 O ILE B 60 N ILE B 53 SHEET 3 B 6 TYR B 10 ILE B 17 1 N PHE B 12 O LYS B 61 SHEET 4 B 6 GLY B 86 ASP B 92 1 O VAL B 90 N ILE B 17 SHEET 5 B 6 VAL B 118 ASN B 124 1 O ASN B 124 N TYR B 91 SHEET 6 B 6 SER B 149 THR B 153 1 O THR B 153 N GLY B 123 LINK C ILE A 119 N MSE A 120 1555 1555 1.33 LINK C MSE A 120 N LEU A 121 1555 1555 1.33 LINK C ILE B 119 N MSE B 120 1555 1555 1.33 LINK C MSE B 120 N LEU B 121 1555 1555 1.33 LINK C VAL C 488 N MSE C 489 1555 1555 1.33 LINK C MSE C 489 N GLU C 490 1555 1555 1.33 LINK C VAL D 488 N MSE D 489 1555 1555 1.32 LINK C MSE D 489 N GLU D 490 1555 1555 1.33 LINK OG SER A 25 MG MG A 950 1555 1555 2.22 LINK OG1 THR A 43 MG MG A 950 1555 1555 1.94 LINK O2G GTP A 900 MG MG A 950 1555 1555 2.32 LINK O2B GTP A 900 MG MG A 950 1555 1555 2.28 LINK MG MG A 950 O HOH A 951 1555 1555 2.31 LINK OG SER B 25 MG MG B 950 1555 1555 2.23 LINK OG1 THR B 43 MG MG B 950 1555 1555 2.24 LINK O2G GTP B 900 MG MG B 950 1555 1555 2.29 LINK O2B GTP B 900 MG MG B 950 1555 1555 2.15 LINK MG MG B 950 O HOH B 986 1555 1555 2.03 CISPEP 1 VAL C 498 PRO C 499 0 -12.25 CISPEP 2 VAL D 498 PRO D 499 0 3.25 SITE 1 AC1 5 SER A 25 THR A 43 ASP A 66 GTP A 900 SITE 2 AC1 5 HOH A 951 SITE 1 AC2 5 SER B 25 THR B 43 ASP B 66 GTP B 900 SITE 2 AC2 5 HOH B 986 SITE 1 AC3 25 SER A 20 GLY A 21 VAL A 22 GLY A 23 SITE 2 AC3 25 LYS A 24 SER A 25 ASN A 26 PHE A 36 SITE 3 AC3 25 ASN A 37 LEU A 38 SER A 40 SER A 42 SITE 4 AC3 25 THR A 43 ALA A 68 GLY A 69 ASN A 124 SITE 5 AC3 25 LYS A 125 ASP A 127 LEU A 128 SER A 154 SITE 6 AC3 25 ALA A 155 LEU A 156 MG A 950 HOH A 951 SITE 7 AC3 25 HOH A 964 SITE 1 AC4 25 SER B 20 GLY B 21 VAL B 22 GLY B 23 SITE 2 AC4 25 LYS B 24 SER B 25 ASN B 26 PHE B 36 SITE 3 AC4 25 ASN B 37 LEU B 38 SER B 40 SER B 42 SITE 4 AC4 25 THR B 43 ALA B 68 GLY B 69 ASN B 124 SITE 5 AC4 25 LYS B 125 ASP B 127 LEU B 128 SER B 154 SITE 6 AC4 25 ALA B 155 LEU B 156 MG B 950 HOH B 958 SITE 7 AC4 25 HOH B 986 CRYST1 64.364 91.149 113.099 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015537 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010971 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008842 0.00000