PDB Short entry for 5SZK HEADER ENDOCYTOSIS 14-AUG-16 5SZK TITLE STRUCTURE OF HUMAN N-TERMINALLY ENGINEERED RAB1B IN COMPLEX WITH THE TITLE 2 BMERB DOMAIN OF MICAL-CL COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICAL C-TERMINAL-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ERK2-BINDING TESTICULAR PROTEIN 1,EBITEIN-1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RAS-RELATED PROTEIN RAB-1B; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MICALCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RAB1B; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MICAL-CL, DUF3585, MICAL, RAB EFFECTOR, RAB1B, PROTEIN TRANSPORT, KEYWDS 2 ENDOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.RAI,A.OPRISKO,J.CAMPOS,Y.FU,T.FRIESE,A.ITZEN,R.S.GOODY,E.M.GAZDAG, AUTHOR 2 M.P.MUELLER REVDAT 5 17-JAN-24 5SZK 1 REMARK REVDAT 4 06-SEP-17 5SZK 1 REMARK REVDAT 3 14-SEP-16 5SZK 1 JRNL REVDAT 2 07-SEP-16 5SZK 1 JRNL REVDAT 1 24-AUG-16 5SZK 0 JRNL AUTH A.RAI,A.OPRISKO,J.CAMPOS,Y.FU,T.FRIESE,A.ITZEN,R.S.GOODY, JRNL AUTH 2 E.M.GAZDAG,M.P.MULLER JRNL TITL BMERB DOMAINS ARE BIVALENT RAB8 FAMILY EFFECTORS EVOLVED BY JRNL TITL 2 GENE DUPLICATION. JRNL REF ELIFE V. 5 2016 JRNL REFN ESSN 2050-084X JRNL PMID 27552051 JRNL DOI 10.7554/ELIFE.18675 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10-2155_1692: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 12904 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.8254 - 4.7866 1.00 2550 135 0.1883 0.2304 REMARK 3 2 4.7866 - 3.7999 1.00 2467 129 0.1897 0.2254 REMARK 3 3 3.7999 - 3.3198 1.00 2410 127 0.2198 0.3240 REMARK 3 4 3.3198 - 3.0163 1.00 2425 128 0.2581 0.3278 REMARK 3 5 3.0163 - 2.8001 1.00 2406 127 0.3075 0.3838 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2626 REMARK 3 ANGLE : 1.178 3527 REMARK 3 CHIRALITY : 0.061 395 REMARK 3 PLANARITY : 0.005 447 REMARK 3 DIHEDRAL : 18.209 1630 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN B AND RESSEQ 1:173) REMARK 3 ORIGIN FOR THE GROUP (A): 22.5177 14.5260 -15.0487 REMARK 3 T TENSOR REMARK 3 T11: 0.5377 T22: 0.5346 REMARK 3 T33: 0.4714 T12: -0.1804 REMARK 3 T13: 0.1160 T23: -0.1395 REMARK 3 L TENSOR REMARK 3 L11: 2.7213 L22: 5.2630 REMARK 3 L33: 3.9862 L12: 1.4147 REMARK 3 L13: 1.0201 L23: 0.7362 REMARK 3 S TENSOR REMARK 3 S11: -0.3583 S12: 0.4679 S13: -0.2449 REMARK 3 S21: -0.7288 S22: 0.7941 S23: -0.3394 REMARK 3 S31: 0.0977 S32: 0.4445 S33: 0.6608 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 531:681) REMARK 3 ORIGIN FOR THE GROUP (A): 28.0475 40.8991 -10.3750 REMARK 3 T TENSOR REMARK 3 T11: 0.4257 T22: 0.5177 REMARK 3 T33: 0.5115 T12: -0.0722 REMARK 3 T13: -0.1237 T23: 0.1026 REMARK 3 L TENSOR REMARK 3 L11: 1.1977 L22: 2.3485 REMARK 3 L33: 0.8884 L12: 0.6994 REMARK 3 L13: -0.4193 L23: 0.3170 REMARK 3 S TENSOR REMARK 3 S11: -0.3918 S12: 0.0690 S13: 0.0989 REMARK 3 S21: -0.2762 S22: 0.1769 S23: -0.0662 REMARK 3 S31: -0.1985 S32: -0.0848 S33: -0.0032 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5SZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000220735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91908 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12904 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 44.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.20 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.07900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.80 REMARK 200 R MERGE FOR SHELL (I) : 1.11000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.450 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3NKV, 5SZG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 7.5, 0.2M SODIUM REMARK 280 MALONATE AND 20% (W/V) PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.71500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.71500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 31.11500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.51500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.11500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.51500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.71500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.11500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.51500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.71500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.11500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.51500 REMARK 290 SMTRY3 8 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 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 531 REMARK 465 HIS A 532 REMARK 465 GLY A 574 REMARK 465 GLU A 575 REMARK 465 ALA A 576 REMARK 465 ASP A 577 REMARK 465 SER A 578 REMARK 465 GLY A 579 REMARK 465 THR A 580 REMARK 465 GLN A 581 REMARK 465 PHE A 681 REMARK 465 GLU A 682 REMARK 465 SER A 683 REMARK 465 GLY B -1 REMARK 465 HIS B 0 REMARK 465 GLY B 174 REMARK 465 PRO B 175 REMARK 465 GLY B 176 REMARK 465 ALA B 177 REMARK 465 ALA B 178 REMARK 465 SER B 179 REMARK 465 GLY B 180 REMARK 465 GLY B 181 REMARK 465 GLU B 182 REMARK 465 ARG B 183 REMARK 465 PRO B 184 REMARK 465 ASN B 185 REMARK 465 LEU B 186 REMARK 465 LYS B 187 REMARK 465 ILE B 188 REMARK 465 ASP B 189 REMARK 465 SER B 190 REMARK 465 THR B 191 REMARK 465 PRO B 192 REMARK 465 VAL B 193 REMARK 465 LYS B 194 REMARK 465 PRO B 195 REMARK 465 ALA B 196 REMARK 465 GLY B 197 REMARK 465 GLY B 198 REMARK 465 GLY B 199 REMARK 465 CYS B 200 REMARK 465 CYS B 201 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 ARG A 573 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 582 CG OD1 OD2 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 A 671 NZ LYS A 675 2.10 REMARK 500 OD1 ASN B 154 OG1 THR B 156 2.17 REMARK 500 O GLN A 535 N GLU A 537 2.19 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 536 3.69 36.73 REMARK 500 ASP B 53 -118.62 53.38 REMARK 500 VAL B 130 -35.83 -130.26 REMARK 500 ALA B 155 7.17 89.78 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 GLU A 536 GLU A 537 134.41 REMARK 500 SER B 142 LEU B 143 129.30 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 B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 22 OG REMARK 620 2 THR B 40 OG1 76.5 REMARK 620 3 GNP B 302 O2G 128.4 72.8 REMARK 620 4 GNP B 302 O2B 81.4 122.4 81.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP B 302 DBREF 5SZK A 534 683 UNP Q6ZW33 MICLK_HUMAN 534 683 DBREF 5SZK B 1 201 UNP Q9H0U4 RAB1B_HUMAN 1 201 SEQADV 5SZK GLY A 531 UNP Q6ZW33 EXPRESSION TAG SEQADV 5SZK HIS A 532 UNP Q6ZW33 EXPRESSION TAG SEQADV 5SZK MET A 533 UNP Q6ZW33 EXPRESSION TAG SEQADV 5SZK GLY B -1 UNP Q9H0U4 EXPRESSION TAG SEQADV 5SZK HIS B 0 UNP Q9H0U4 EXPRESSION TAG SEQADV 5SZK ALA B 2 UNP Q9H0U4 ASN 2 ENGINEERED MUTATION SEQADV 5SZK LYS B 3 UNP Q9H0U4 PRO 3 ENGINEERED MUTATION SEQADV 5SZK THR B 4 UNP Q9H0U4 GLU 4 ENGINEERED MUTATION SEQRES 1 A 153 GLY HIS MET LYS GLN GLU GLU LEU LYS ARG LEU TYR LYS SEQRES 2 A 153 ALA GLN ALA ILE GLN ARG GLN LEU GLU GLU VAL GLU GLU SEQRES 3 A 153 ARG GLN ARG ALA SER GLU ILE GLN GLY VAL ARG LEU GLU SEQRES 4 A 153 LYS ALA LEU ARG GLY GLU ALA ASP SER GLY THR GLN ASP SEQRES 5 A 153 GLU ALA GLN LEU LEU GLN GLU TRP PHE LYS LEU VAL LEU SEQRES 6 A 153 GLU LYS ASN LYS LEU MET ARG TYR GLU SER GLU LEU LEU SEQRES 7 A 153 ILE MET ALA GLN GLU LEU GLU LEU GLU ASP HIS GLN SER SEQRES 8 A 153 ARG LEU GLU GLN LYS LEU ARG GLU LYS MET LEU LYS GLU SEQRES 9 A 153 GLU SER GLN LYS ASP GLU LYS ASP LEU ASN GLU GLU GLN SEQRES 10 A 153 GLU VAL PHE THR GLU LEU MET GLN VAL ILE GLU GLN ARG SEQRES 11 A 153 ASP LYS LEU VAL ASP SER LEU GLU GLU GLN ARG ILE ARG SEQRES 12 A 153 GLU LYS ALA GLU ASP GLN HIS PHE GLU SER SEQRES 1 B 203 GLY HIS MET ALA LYS THR TYR ASP TYR LEU PHE LYS LEU SEQRES 2 B 203 LEU LEU ILE GLY ASP SER GLY VAL GLY LYS SER CYS LEU SEQRES 3 B 203 LEU LEU ARG PHE ALA ASP ASP THR TYR THR GLU SER TYR SEQRES 4 B 203 ILE SER THR ILE GLY VAL ASP PHE LYS ILE ARG THR ILE SEQRES 5 B 203 GLU LEU ASP GLY LYS THR ILE LYS LEU GLN ILE TRP ASP SEQRES 6 B 203 THR ALA GLY GLN GLU ARG PHE ARG THR ILE THR SER SER SEQRES 7 B 203 TYR TYR ARG GLY ALA HIS GLY ILE ILE VAL VAL TYR ASP SEQRES 8 B 203 VAL THR ASP GLN GLU SER TYR ALA ASN VAL LYS GLN TRP SEQRES 9 B 203 LEU GLN GLU ILE ASP ARG TYR ALA SER GLU ASN VAL ASN SEQRES 10 B 203 LYS LEU LEU VAL GLY ASN LYS SER ASP LEU THR THR LYS SEQRES 11 B 203 LYS VAL VAL ASP ASN THR THR ALA LYS GLU PHE ALA ASP SEQRES 12 B 203 SER LEU GLY ILE PRO PHE LEU GLU THR SER ALA LYS ASN SEQRES 13 B 203 ALA THR ASN VAL GLU GLN ALA PHE MET THR MET ALA ALA SEQRES 14 B 203 GLU ILE LYS LYS ARG MET GLY PRO GLY ALA ALA SER GLY SEQRES 15 B 203 GLY GLU ARG PRO ASN LEU LYS ILE ASP SER THR PRO VAL SEQRES 16 B 203 LYS PRO ALA GLY GLY GLY CYS CYS HET MG B 301 1 HET GNP B 302 32 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER FORMUL 3 MG MG 2+ FORMUL 4 GNP C10 H17 N6 O13 P3 FORMUL 5 HOH *3(H2 O) HELIX 1 AA1 GLU A 537 ALA A 571 1 35 HELIX 2 AA2 GLU A 583 LEU A 632 1 50 HELIX 3 AA3 ASP A 639 ASP A 678 1 40 HELIX 4 AA4 GLY B 20 ASP B 31 1 12 HELIX 5 AA5 GLN B 67 ARG B 69 5 3 HELIX 6 AA6 PHE B 70 SER B 76 1 7 HELIX 7 AA7 TYR B 77 ARG B 79 5 3 HELIX 8 AA8 ASP B 92 ASN B 98 1 7 HELIX 9 AA9 ASN B 98 ALA B 110 1 13 HELIX 10 AB1 ASP B 132 ASP B 141 1 10 HELIX 11 AB2 ASN B 157 ARG B 172 1 16 SHEET 1 AA1 6 VAL B 43 LEU B 52 0 SHEET 2 AA1 6 LYS B 55 THR B 64 -1 O ASP B 63 N ASP B 44 SHEET 3 AA1 6 TYR B 7 GLY B 15 1 N LEU B 11 O GLN B 60 SHEET 4 AA1 6 GLY B 83 ASP B 89 1 O ILE B 85 N LEU B 12 SHEET 5 AA1 6 ASN B 115 ASN B 121 1 O ASN B 121 N TYR B 88 SHEET 6 AA1 6 PHE B 147 GLU B 149 1 O LEU B 148 N GLY B 120 LINK OG SER B 22 MG MG B 301 1555 1555 2.23 LINK OG1 THR B 40 MG MG B 301 1555 1555 2.32 LINK MG MG B 301 O2G GNP B 302 1555 1555 1.98 LINK MG MG B 301 O2B GNP B 302 1555 1555 2.14 SITE 1 AC1 4 SER B 22 ILE B 38 THR B 40 GNP B 302 SITE 1 AC2 22 SER B 17 GLY B 18 VAL B 19 GLY B 20 SITE 2 AC2 22 LYS B 21 SER B 22 CYS B 23 TYR B 33 SITE 3 AC2 22 THR B 34 GLU B 35 SER B 36 TYR B 37 SITE 4 AC2 22 SER B 39 THR B 40 GLY B 66 ASN B 121 SITE 5 AC2 22 LYS B 122 ASP B 124 SER B 151 ALA B 152 SITE 6 AC2 22 LYS B 153 MG B 301 CRYST1 62.230 117.030 139.430 90.00 90.00 90.00 C 2 2 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 0.016069 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008545 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007172 0.00000