HEADER ENDOCYTOSIS 14-AUG-16 5SZI TITLE STRUCTURE OF HUMAN RAB8A IN COMPLEX WITH THE BMERB DOMAIN OF MICAL-CL COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-8A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ONCOGENE C-MEL; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: MICAL C-TERMINAL-LIKE PROTEIN; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: ERK2-BINDING TESTICULAR PROTEIN 1,EBITEIN-1; COMPND 10 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: RAB8A, MEL, RAB8; 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: MICALCL; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MICAL-CL, DUF3585, MICAL, RAB EFFECTOR, RAB8A, TRANSPORT PROTEIN, KEYWDS 2 ENDOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.RAI,A.OPRISKO,J.CAMPOS,Y.FU,T.FRIESE,A.ITZEN,R.S.GOODY,M.P.MUELLER, AUTHOR 2 E.M.GAZDAG REVDAT 5 17-JAN-24 5SZI 1 REMARK REVDAT 4 06-SEP-17 5SZI 1 REMARK REVDAT 3 14-SEP-16 5SZI 1 JRNL REVDAT 2 07-SEP-16 5SZI 1 JRNL REVDAT 1 24-AUG-16 5SZI 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. 2.85 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 12808 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 641 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 45.9581 - 4.8722 1.00 2535 134 0.2262 0.2817 REMARK 3 2 4.8722 - 3.8678 1.00 2439 128 0.2213 0.2930 REMARK 3 3 3.8678 - 3.3791 1.00 2409 127 0.2448 0.2836 REMARK 3 4 3.3791 - 3.0702 1.00 2404 127 0.2769 0.2792 REMARK 3 5 3.0702 - 2.8502 1.00 2380 125 0.3111 0.3500 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.840 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 : 0.009 2487 REMARK 3 ANGLE : 1.175 3361 REMARK 3 CHIRALITY : 0.061 385 REMARK 3 PLANARITY : 0.005 433 REMARK 3 DIHEDRAL : 20.336 1508 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 2:400) REMARK 3 ORIGIN FOR THE GROUP (A): 8.4498 45.9171 -14.3057 REMARK 3 T TENSOR REMARK 3 T11: 0.4312 T22: 0.4485 REMARK 3 T33: 0.3783 T12: -0.1764 REMARK 3 T13: -0.1318 T23: -0.0427 REMARK 3 L TENSOR REMARK 3 L11: 1.7070 L22: 4.9765 REMARK 3 L33: 3.2930 L12: 0.3370 REMARK 3 L13: -1.2669 L23: -3.7608 REMARK 3 S TENSOR REMARK 3 S11: -0.5241 S12: 0.3991 S13: -0.0477 REMARK 3 S21: -0.1895 S22: 0.7919 S23: -0.2356 REMARK 3 S31: -0.0978 S32: -0.3470 S33: 0.7031 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 5SZI 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_1000220790. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3-8.7 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) : 1.00009 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 : 12810 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : 0.09200 REMARK 200 FOR THE DATA SET : 16.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.78000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: 4LHW, 5SZG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS TRIS PROPANE 0.2M TRI SODIUM REMARK 280 CITRATE 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 69.57500 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 69.57500 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 31.20000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.20000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.20000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.20000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.57500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.20000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.20000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.57500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.20000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.20000 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: 2550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17340 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 -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 177 REMARK 465 GLU A 178 REMARK 465 GLY A 179 REMARK 465 ASN A 180 REMARK 465 SER A 181 REMARK 465 PRO A 182 REMARK 465 GLN A 183 REMARK 465 GLY A 184 REMARK 465 SER A 185 REMARK 465 ASN A 186 REMARK 465 GLN A 187 REMARK 465 GLY A 188 REMARK 465 VAL A 189 REMARK 465 LYS A 190 REMARK 465 ILE A 191 REMARK 465 THR A 192 REMARK 465 PRO A 193 REMARK 465 ASP A 194 REMARK 465 GLN A 195 REMARK 465 GLN A 196 REMARK 465 LYS A 197 REMARK 465 ARG A 198 REMARK 465 SER A 199 REMARK 465 SER A 200 REMARK 465 PHE A 201 REMARK 465 PHE A 202 REMARK 465 ARG A 203 REMARK 465 CYS A 204 REMARK 465 VAL A 205 REMARK 465 LEU A 206 REMARK 465 LEU A 207 REMARK 465 GLY B 531 REMARK 465 HIS B 532 REMARK 465 ARG B 573 REMARK 465 GLY B 574 REMARK 465 GLU B 575 REMARK 465 ALA B 576 REMARK 465 ASP B 577 REMARK 465 SER B 578 REMARK 465 GLY B 579 REMARK 465 THR B 580 REMARK 465 GLN B 581 REMARK 465 GLU B 682 REMARK 465 SER B 683 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 GLU A 51 CG CD OE1 OE2 REMARK 470 LEU A 52 CG CD1 CD2 REMARK 470 ARG A 56 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 ARG A 104 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 108 CG CD OE1 OE2 REMARK 470 LYS A 116 CG CD CE NZ REMARK 470 LYS A 128 CG CD CE NZ REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 LYS A 146 CG CD CE NZ REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 LYS A 153 CG CD CE NZ REMARK 470 GLU A 159 CG CD OE1 OE2 REMARK 470 LYS A 170 CG CD CE NZ REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 LYS A 175 CG CD CE NZ REMARK 470 LYS A 176 CG CD CE NZ REMARK 470 ARG B 549 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 559 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 562 CG CD OE1 OE2 REMARK 470 GLU B 569 CG CD OE1 OE2 REMARK 470 LYS B 570 CG CD CE NZ REMARK 470 LEU B 572 CG CD1 CD2 REMARK 470 ASP B 582 CG OD1 OD2 REMARK 470 GLN B 585 CG CD OE1 NE2 REMARK 470 LEU B 587 CG CD1 CD2 REMARK 470 GLN B 588 CG CD OE1 NE2 REMARK 470 LYS B 592 CG CD CE NZ REMARK 470 LYS B 597 CG CD CE NZ REMARK 470 LYS B 599 CG CD CE NZ REMARK 470 LYS B 633 CG CD CE NZ REMARK 470 LYS B 638 CG CD CE NZ REMARK 470 GLU B 640 CG CD OE1 OE2 REMARK 470 LYS B 641 CG CD CE NZ REMARK 470 ASP B 642 CG OD1 OD2 REMARK 470 GLU B 648 CG CD OE1 OE2 REMARK 470 LYS B 662 CG CD CE NZ REMARK 470 ARG B 671 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 675 CG CD CE NZ REMARK 470 ASP B 678 CG OD1 OD2 REMARK 470 GLN B 679 CG CD OE1 NE2 REMARK 470 PHE B 681 CG CD1 CD2 CE1 CE2 CZ 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 THR A 72 OG1 THR A 75 2.06 REMARK 500 NH2 ARG B 602 OE2 GLU B 677 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 137 CD GLU A 137 OE2 -0.075 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 THR A 72 -74.53 -29.13 REMARK 500 GLU A 159 -77.65 -36.42 REMARK 500 GLU B 536 15.74 47.97 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 B 536 GLU B 537 138.91 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 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 22 OG1 REMARK 620 2 THR A 40 OG1 80.5 REMARK 620 3 GNP A 301 O3G 158.4 96.1 REMARK 620 4 GNP A 301 O2B 75.3 139.2 94.6 REMARK 620 5 HOH A 401 O 96.5 108.8 104.7 106.2 REMARK 620 6 HOH A 402 O 76.8 73.1 81.8 69.7 172.7 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 GNP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 302 DBREF 5SZI A 1 207 UNP P61006 RAB8A_HUMAN 1 207 DBREF 5SZI B 534 683 UNP Q6ZW33 MICLK_HUMAN 534 683 SEQADV 5SZI GLY A -1 UNP P61006 EXPRESSION TAG SEQADV 5SZI HIS A 0 UNP P61006 EXPRESSION TAG SEQADV 5SZI GLY B 531 UNP Q6ZW33 EXPRESSION TAG SEQADV 5SZI HIS B 532 UNP Q6ZW33 EXPRESSION TAG SEQADV 5SZI MET B 533 UNP Q6ZW33 EXPRESSION TAG SEQRES 1 A 209 GLY HIS MET ALA LYS THR TYR ASP TYR LEU PHE LYS LEU SEQRES 2 A 209 LEU LEU ILE GLY ASP SER GLY VAL GLY LYS THR CYS VAL SEQRES 3 A 209 LEU PHE ARG PHE SER GLU ASP ALA PHE ASN SER THR PHE SEQRES 4 A 209 ILE SER THR ILE GLY ILE ASP PHE LYS ILE ARG THR ILE SEQRES 5 A 209 GLU LEU ASP GLY LYS ARG ILE LYS LEU GLN ILE TRP ASP SEQRES 6 A 209 THR ALA GLY GLN GLU ARG PHE ARG THR ILE THR THR ALA SEQRES 7 A 209 TYR TYR ARG GLY ALA MET GLY ILE MET LEU VAL TYR ASP SEQRES 8 A 209 ILE THR ASN GLU LYS SER PHE ASP ASN ILE ARG ASN TRP SEQRES 9 A 209 ILE ARG ASN ILE GLU GLU HIS ALA SER ALA ASP VAL GLU SEQRES 10 A 209 LYS MET ILE LEU GLY ASN LYS CYS ASP VAL ASN ASP LYS SEQRES 11 A 209 ARG GLN VAL SER LYS GLU ARG GLY GLU LYS LEU ALA LEU SEQRES 12 A 209 ASP TYR GLY ILE LYS PHE MET GLU THR SER ALA LYS ALA SEQRES 13 A 209 ASN ILE ASN VAL GLU ASN ALA PHE PHE THR LEU ALA ARG SEQRES 14 A 209 ASP ILE LYS ALA LYS MET ASP LYS LYS LEU GLU GLY ASN SEQRES 15 A 209 SER PRO GLN GLY SER ASN GLN GLY VAL LYS ILE THR PRO SEQRES 16 A 209 ASP GLN GLN LYS ARG SER SER PHE PHE ARG CYS VAL LEU SEQRES 17 A 209 LEU SEQRES 1 B 153 GLY HIS MET LYS GLN GLU GLU LEU LYS ARG LEU TYR LYS SEQRES 2 B 153 ALA GLN ALA ILE GLN ARG GLN LEU GLU GLU VAL GLU GLU SEQRES 3 B 153 ARG GLN ARG ALA SER GLU ILE GLN GLY VAL ARG LEU GLU SEQRES 4 B 153 LYS ALA LEU ARG GLY GLU ALA ASP SER GLY THR GLN ASP SEQRES 5 B 153 GLU ALA GLN LEU LEU GLN GLU TRP PHE LYS LEU VAL LEU SEQRES 6 B 153 GLU LYS ASN LYS LEU MET ARG TYR GLU SER GLU LEU LEU SEQRES 7 B 153 ILE MET ALA GLN GLU LEU GLU LEU GLU ASP HIS GLN SER SEQRES 8 B 153 ARG LEU GLU GLN LYS LEU ARG GLU LYS MET LEU LYS GLU SEQRES 9 B 153 GLU SER GLN LYS ASP GLU LYS ASP LEU ASN GLU GLU GLN SEQRES 10 B 153 GLU VAL PHE THR GLU LEU MET GLN VAL ILE GLU GLN ARG SEQRES 11 B 153 ASP LYS LEU VAL ASP SER LEU GLU GLU GLN ARG ILE ARG SEQRES 12 B 153 GLU LYS ALA GLU ASP GLN HIS PHE GLU SER HET GNP A 301 32 HET MG A 302 1 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 3 GNP C10 H17 N6 O13 P3 FORMUL 4 MG MG 2+ FORMUL 5 HOH *2(H2 O) HELIX 1 AA1 GLY A 20 ASP A 31 1 12 HELIX 2 AA2 GLN A 67 TYR A 77 1 11 HELIX 3 AA3 ASN A 92 ASN A 98 1 7 HELIX 4 AA4 ASN A 98 ALA A 110 1 13 HELIX 5 AA5 SER A 132 GLY A 144 1 13 HELIX 6 AA6 ASN A 157 LYS A 176 1 20 HELIX 7 AA7 GLU B 537 LEU B 572 1 36 HELIX 8 AA8 GLU B 583 LYS B 633 1 51 HELIX 9 AA9 GLU B 634 LYS B 638 5 5 HELIX 10 AB1 ASP B 639 GLN B 679 1 41 SHEET 1 AA1 6 ILE A 43 LEU A 52 0 SHEET 2 AA1 6 LYS A 55 THR A 64 -1 O ILE A 61 N LYS A 46 SHEET 3 AA1 6 TYR A 7 ILE A 14 1 N LEU A 11 O GLN A 60 SHEET 4 AA1 6 GLY A 83 ASP A 89 1 O VAL A 87 N ILE A 14 SHEET 5 AA1 6 MET A 117 ASN A 121 1 O ASN A 121 N TYR A 88 SHEET 6 AA1 6 LYS A 146 GLU A 149 1 O LYS A 146 N ILE A 118 LINK OG1 THR A 22 MG MG A 302 1555 1555 1.88 LINK OG1 THR A 40 MG MG A 302 1555 1555 2.36 LINK O3G GNP A 301 MG MG A 302 1555 1555 1.83 LINK O2B GNP A 301 MG MG A 302 1555 1555 2.12 LINK MG MG A 302 O HOH A 401 1555 1555 2.01 LINK MG MG A 302 O HOH A 402 1555 1555 2.20 SITE 1 AC1 23 SER A 17 GLY A 18 VAL A 19 GLY A 20 SITE 2 AC1 23 LYS A 21 THR A 22 CYS A 23 PHE A 33 SITE 3 AC1 23 ASN A 34 SER A 35 PHE A 37 SER A 39 SITE 4 AC1 23 THR A 40 GLY A 66 ASN A 121 LYS A 122 SITE 5 AC1 23 ASP A 124 SER A 151 ALA A 152 LYS A 153 SITE 6 AC1 23 MG A 302 HOH A 401 HOH A 402 SITE 1 AC2 5 THR A 22 THR A 40 GNP A 301 HOH A 401 SITE 2 AC2 5 HOH A 402 CRYST1 62.400 122.400 139.150 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 0.016026 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007186 0.00000