PDB Short entry for 1Z0K HEADER PROTEIN TRANSPORT 01-MAR-05 1Z0K TITLE STRUCTURE OF GTP-BOUND RAB4Q67L GTPASE IN COMPLEX WITH THE CENTRAL RAB TITLE 2 BINDING DOMAIN OF RABENOSYN-5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING PROTEIN; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FYVE-FINGER-CONTAINING RAB5 EFFECTOR PROTEIN RABENOSYN-5; COMPND 7 CHAIN: B, D; COMPND 8 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: RAB4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON PLUS-RIL CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: 6XHIS FUSION-PET SYSTEM,; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET28A; 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; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: GST FUSION-PGEX SYSTEM; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PGEX6P1 KEYWDS RAB GTPASES, RAB4, RABENOSYN, EFFECTOR COMPLEX, VESICULAR KEYWDS 2 TRAFFICKING, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.EATHIRAJ,X.PAN,C.RITACCO,D.G.LAMBRIGHT REVDAT 5 03-APR-24 1Z0K 1 REMARK REVDAT 4 14-FEB-24 1Z0K 1 REMARK REVDAT 3 20-OCT-21 1Z0K 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1Z0K 1 VERSN REVDAT 1 26-JUL-05 1Z0K 0 JRNL AUTH S.EATHIRAJ,X.PAN,C.RITACCO,D.G.LAMBRIGHT JRNL TITL STRUCTURAL BASIS OF FAMILY-WIDE RAB GTPASE RECOGNITION BY JRNL TITL 2 RABENOSYN-5. JRNL REF NATURE V. 436 415 2005 JRNL REFN ISSN 0028-0836 JRNL PMID 16034420 JRNL DOI 10.1038/NATURE03798 REMARK 2 REMARK 2 RESOLUTION. 1.92 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 38744 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2072 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) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2770 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 144 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3573 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 457 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.20000 REMARK 3 B22 (A**2) : 1.20000 REMARK 3 B33 (A**2) : -1.80000 REMARK 3 B12 (A**2) : 0.60000 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): 0.188 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.165 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.500 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3708 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5023 ; 1.302 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 5.341 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;36.918 ;24.833 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 622 ;12.886 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;19.757 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 560 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2780 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1891 ; 0.192 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2570 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 487 ; 0.143 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.126 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 48 ; 0.186 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 41 ; 0.148 ; 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): 2340 ; 0.626 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3592 ; 1.053 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1590 ; 1.243 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1431 ; 1.953 ; 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 : NULL 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 1Z0K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42193 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: RAB4 GTPASE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 200MM AMMONIUM FLUORIDE, REMARK 280 50MM MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.87967 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 91.75933 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 91.75933 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.87967 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 REMARK 465 GLY B 435 REMARK 465 PRO B 436 REMARK 465 LEU B 437 REMARK 465 GLY B 438 REMARK 465 SER B 439 REMARK 465 ALA B 440 REMARK 465 GLU B 502 REMARK 465 LYS B 503 REMARK 465 GLY C 1 REMARK 465 SER C 2 REMARK 465 GLU C 3 REMARK 465 THR C 4 REMARK 465 GLY D 435 REMARK 465 PRO D 436 REMARK 465 LEU D 437 REMARK 465 GLY D 438 REMARK 465 SER D 439 REMARK 465 ALA D 440 REMARK 465 GLU D 502 REMARK 465 LYS D 503 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 ASN A 38 CG OD1 ND2 REMARK 470 HIS A 39 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 79 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 94 CG CD OE1 OE2 REMARK 470 GLN A 141 CG CD OE1 NE2 REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 GLN B 450 CG CD OE1 NE2 REMARK 470 GLN B 452 CG CD OE1 NE2 REMARK 470 GLN B 498 CG CD OE1 NE2 REMARK 470 THR B 501 OG1 CG2 REMARK 470 LYS C 32 CG CD CE NZ REMARK 470 LYS C 55 CG CD CE NZ REMARK 470 GLU C 68 CG CD OE1 OE2 REMARK 470 ASP C 126 CG OD1 OD2 REMARK 470 GLU D 441 CG CD OE1 OE2 REMARK 470 GLN D 450 CG CD OE1 NE2 REMARK 470 GLN D 452 CG CD OE1 NE2 REMARK 470 SER D 456 OG REMARK 470 ARG D 483 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 490 CG CD NE CZ NH1 NH2 REMARK 470 GLN D 498 CG CD OE1 NE2 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 ILE A 41 39.62 -98.47 REMARK 500 LEU A 125 51.82 -101.32 REMARK 500 SER B 447 85.42 -66.75 REMARK 500 GLN B 450 52.74 30.79 REMARK 500 ALA C 110 -94.07 -85.54 REMARK 500 LYS C 122 33.97 74.57 REMARK 500 LEU C 125 35.22 -89.24 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 A1201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 22 OG REMARK 620 2 THR A 40 OG1 74.2 REMARK 620 3 GTP A1200 O2B 91.2 162.5 REMARK 620 4 GTP A1200 O2G 154.0 87.8 102.5 REMARK 620 5 HOH A1207 O 92.2 89.0 101.4 106.3 REMARK 620 6 HOH A1212 O 77.7 76.8 90.8 80.1 164.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C2201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER C 22 OG REMARK 620 2 THR C 40 OG1 83.9 REMARK 620 3 GTP C2200 O2B 93.8 172.5 REMARK 620 4 GTP C2200 O2G 163.8 82.6 100.8 REMARK 620 5 HOH C2208 O 80.4 87.8 98.8 90.1 REMARK 620 6 HOH C2222 O 89.9 83.1 89.8 97.3 167.4 REMARK 620 N 1 2 3 4 5 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 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 2201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP C 2200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES D 1001 DBREF 1Z0K A 2 172 UNP P20338 RAB4A_HUMAN 2 172 DBREF 1Z0K C 2 172 UNP P20338 RAB4A_HUMAN 2 172 DBREF 1Z0K B 440 503 UNP Q59EY8 Q59EY8_HUMAN 440 503 DBREF 1Z0K D 440 503 UNP Q59EY8 Q59EY8_HUMAN 440 503 SEQADV 1Z0K GLY A 1 UNP P20338 CLONING ARTIFACT SEQADV 1Z0K LEU A 67 UNP P20338 GLN 67 ENGINEERED MUTATION SEQADV 1Z0K GLY C 1 UNP P20338 CLONING ARTIFACT SEQADV 1Z0K LEU C 67 UNP P20338 GLN 67 ENGINEERED MUTATION SEQADV 1Z0K GLY B 435 UNP Q59EY8 CLONING ARTIFACT SEQADV 1Z0K PRO B 436 UNP Q59EY8 CLONING ARTIFACT SEQADV 1Z0K LEU B 437 UNP Q59EY8 CLONING ARTIFACT SEQADV 1Z0K GLY B 438 UNP Q59EY8 CLONING ARTIFACT SEQADV 1Z0K SER B 439 UNP Q59EY8 CLONING ARTIFACT SEQADV 1Z0K GLY D 435 UNP Q59EY8 CLONING ARTIFACT SEQADV 1Z0K PRO D 436 UNP Q59EY8 CLONING ARTIFACT SEQADV 1Z0K LEU D 437 UNP Q59EY8 CLONING ARTIFACT SEQADV 1Z0K GLY D 438 UNP Q59EY8 CLONING ARTIFACT SEQADV 1Z0K SER D 439 UNP Q59EY8 CLONING ARTIFACT SEQRES 1 A 172 GLY SER GLU THR TYR ASP PHE LEU PHE LYS PHE LEU VAL SEQRES 2 A 172 ILE GLY ASN ALA GLY THR GLY LYS SER CYS LEU LEU HIS SEQRES 3 A 172 GLN PHE ILE GLU LYS LYS PHE LYS ASP ASP SER ASN HIS SEQRES 4 A 172 THR ILE GLY VAL GLU PHE GLY SER LYS ILE ILE ASN VAL SEQRES 5 A 172 GLY GLY LYS TYR VAL LYS LEU GLN ILE TRP ASP THR ALA SEQRES 6 A 172 GLY LEU GLU ARG PHE ARG SER VAL THR ARG SER TYR TYR SEQRES 7 A 172 ARG GLY ALA ALA GLY ALA LEU LEU VAL TYR ASP ILE THR SEQRES 8 A 172 SER ARG GLU THR TYR ASN ALA LEU THR ASN TRP LEU THR SEQRES 9 A 172 ASP ALA ARG MET LEU ALA SER GLN ASN ILE VAL ILE ILE SEQRES 10 A 172 LEU CYS GLY ASN LYS LYS ASP LEU ASP ALA ASP ARG GLU SEQRES 11 A 172 VAL THR PHE LEU GLU ALA SER ARG PHE ALA GLN GLU ASN SEQRES 12 A 172 GLU LEU MET PHE LEU GLU THR SER ALA LEU THR GLY GLU SEQRES 13 A 172 ASP VAL GLU GLU ALA PHE VAL GLN CYS ALA ARG LYS ILE SEQRES 14 A 172 LEU ASN LYS SEQRES 1 B 69 GLY PRO LEU GLY SER ALA GLU GLY TRP LEU PRO LEU SER SEQRES 2 B 69 GLY GLY GLN GLY GLN SER GLU ASP SER ASP PRO LEU LEU SEQRES 3 B 69 GLN GLN ILE HIS ASN ILE THR SER PHE ILE ARG GLN ALA SEQRES 4 B 69 LYS ALA ALA GLY ARG MET ASP GLU VAL ARG THR LEU GLN SEQRES 5 B 69 GLU ASN LEU ARG GLN LEU GLN ASP GLU TYR ASP GLN GLN SEQRES 6 B 69 GLN THR GLU LYS SEQRES 1 C 172 GLY SER GLU THR TYR ASP PHE LEU PHE LYS PHE LEU VAL SEQRES 2 C 172 ILE GLY ASN ALA GLY THR GLY LYS SER CYS LEU LEU HIS SEQRES 3 C 172 GLN PHE ILE GLU LYS LYS PHE LYS ASP ASP SER ASN HIS SEQRES 4 C 172 THR ILE GLY VAL GLU PHE GLY SER LYS ILE ILE ASN VAL SEQRES 5 C 172 GLY GLY LYS TYR VAL LYS LEU GLN ILE TRP ASP THR ALA SEQRES 6 C 172 GLY LEU GLU ARG PHE ARG SER VAL THR ARG SER TYR TYR SEQRES 7 C 172 ARG GLY ALA ALA GLY ALA LEU LEU VAL TYR ASP ILE THR SEQRES 8 C 172 SER ARG GLU THR TYR ASN ALA LEU THR ASN TRP LEU THR SEQRES 9 C 172 ASP ALA ARG MET LEU ALA SER GLN ASN ILE VAL ILE ILE SEQRES 10 C 172 LEU CYS GLY ASN LYS LYS ASP LEU ASP ALA ASP ARG GLU SEQRES 11 C 172 VAL THR PHE LEU GLU ALA SER ARG PHE ALA GLN GLU ASN SEQRES 12 C 172 GLU LEU MET PHE LEU GLU THR SER ALA LEU THR GLY GLU SEQRES 13 C 172 ASP VAL GLU GLU ALA PHE VAL GLN CYS ALA ARG LYS ILE SEQRES 14 C 172 LEU ASN LYS SEQRES 1 D 69 GLY PRO LEU GLY SER ALA GLU GLY TRP LEU PRO LEU SER SEQRES 2 D 69 GLY GLY GLN GLY GLN SER GLU ASP SER ASP PRO LEU LEU SEQRES 3 D 69 GLN GLN ILE HIS ASN ILE THR SER PHE ILE ARG GLN ALA SEQRES 4 D 69 LYS ALA ALA GLY ARG MET ASP GLU VAL ARG THR LEU GLN SEQRES 5 D 69 GLU ASN LEU ARG GLN LEU GLN ASP GLU TYR ASP GLN GLN SEQRES 6 D 69 GLN THR GLU LYS HET MG A1201 1 HET GTP A1200 32 HET MG C2201 1 HET GTP C2200 32 HET MES D1001 12 HETNAM MG MAGNESIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 5 MG 2(MG 2+) FORMUL 6 GTP 2(C10 H16 N5 O14 P3) FORMUL 9 MES C6 H13 N O4 S FORMUL 10 HOH *457(H2 O) HELIX 1 1 GLY A 20 LYS A 31 1 12 HELIX 2 2 LEU A 67 ARG A 69 5 3 HELIX 3 3 PHE A 70 SER A 76 1 7 HELIX 4 4 SER A 92 ALA A 98 1 7 HELIX 5 5 ALA A 98 ALA A 110 1 13 HELIX 6 6 LEU A 125 ARG A 129 5 5 HELIX 7 7 THR A 132 ASN A 143 1 12 HELIX 8 8 ASP A 157 ASN A 171 1 15 HELIX 9 9 ASP B 457 ALA B 476 1 20 HELIX 10 10 ARG B 478 GLN B 500 1 23 HELIX 11 11 GLY C 20 LYS C 31 1 12 HELIX 12 12 LEU C 67 ARG C 69 5 3 HELIX 13 13 PHE C 70 SER C 76 1 7 HELIX 14 14 SER C 92 ALA C 98 1 7 HELIX 15 15 ALA C 98 ALA C 110 1 13 HELIX 16 16 LYS C 123 ARG C 129 5 7 HELIX 17 17 THR C 132 ASN C 143 1 12 HELIX 18 18 ASP C 157 LYS C 172 1 16 HELIX 19 19 ASP D 457 ALA D 476 1 20 HELIX 20 20 ARG D 478 THR D 501 1 24 SHEET 1 A 6 VAL A 43 VAL A 52 0 SHEET 2 A 6 LYS A 55 THR A 64 -1 O LYS A 55 N VAL A 52 SHEET 3 A 6 PHE A 7 GLY A 15 1 N PHE A 11 O GLN A 60 SHEET 4 A 6 GLY A 83 ASP A 89 1 O VAL A 87 N ILE A 14 SHEET 5 A 6 VAL A 115 ASN A 121 1 O CYS A 119 N LEU A 86 SHEET 6 A 6 MET A 146 GLU A 149 1 O MET A 146 N LEU A 118 SHEET 1 B 6 VAL C 43 VAL C 52 0 SHEET 2 B 6 LYS C 55 THR C 64 -1 O LYS C 55 N VAL C 52 SHEET 3 B 6 PHE C 7 GLY C 15 1 N PHE C 7 O LYS C 58 SHEET 4 B 6 GLY C 83 ASP C 89 1 O VAL C 87 N ILE C 14 SHEET 5 B 6 VAL C 115 ASN C 121 1 O CYS C 119 N LEU C 86 SHEET 6 B 6 MET C 146 THR C 150 1 O MET C 146 N LEU C 118 LINK OG SER A 22 MG MG A1201 1555 1555 2.20 LINK OG1 THR A 40 MG MG A1201 1555 1555 2.30 LINK O2B GTP A1200 MG MG A1201 1555 1555 1.82 LINK O2G GTP A1200 MG MG A1201 1555 1555 2.06 LINK MG MG A1201 O HOH A1207 1555 1555 1.94 LINK MG MG A1201 O HOH A1212 1555 1555 2.42 LINK OG SER C 22 MG MG C2201 1555 1555 2.07 LINK OG1 THR C 40 MG MG C2201 1555 1555 2.29 LINK O2B GTP C2200 MG MG C2201 1555 1555 2.03 LINK O2G GTP C2200 MG MG C2201 1555 1555 2.20 LINK MG MG C2201 O HOH C2208 1555 1555 2.04 LINK MG MG C2201 O HOH C2222 1555 1555 2.15 SITE 1 AC1 5 SER A 22 THR A 40 GTP A1200 HOH A1207 SITE 2 AC1 5 HOH A1212 SITE 1 AC2 5 SER C 22 THR C 40 GTP C2200 HOH C2208 SITE 2 AC2 5 HOH C2222 SITE 1 AC3 31 ALA A 17 GLY A 18 THR A 19 GLY A 20 SITE 2 AC3 31 LYS A 21 SER A 22 CYS A 23 PHE A 33 SITE 3 AC3 31 SER A 37 HIS A 39 THR A 40 ALA A 65 SITE 4 AC3 31 GLY A 66 ASN A 121 LYS A 122 ASP A 124 SITE 5 AC3 31 LEU A 125 SER A 151 ALA A 152 LEU A 153 SITE 6 AC3 31 MG A1201 HOH A1207 HOH A1210 HOH A1212 SITE 7 AC3 31 HOH A1262 HOH A1285 HOH A1304 HOH A1317 SITE 8 AC3 31 HOH A1348 ASP C 35 HOH C2300 SITE 1 AC4 24 ALA C 17 GLY C 18 THR C 19 GLY C 20 SITE 2 AC4 24 LYS C 21 SER C 22 CYS C 23 PHE C 33 SITE 3 AC4 24 SER C 37 HIS C 39 THR C 40 GLY C 66 SITE 4 AC4 24 ASN C 121 LYS C 122 ASP C 124 LEU C 125 SITE 5 AC4 24 SER C 151 ALA C 152 LEU C 153 MG C2201 SITE 6 AC4 24 HOH C2208 HOH C2219 HOH C2222 HOH C2247 SITE 1 AC5 7 GLU C 30 GLY D 442 TRP D 443 LEU D 444 SITE 2 AC5 7 LYS D 474 MET D 479 HOH D1072 CRYST1 81.440 81.440 137.639 90.00 90.00 120.00 P 31 2 1 12 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 0.012279 0.007089 0.000000 0.00000 SCALE2 0.000000 0.014179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007265 0.00000