PDB Short entry for 6SQ2 HEADER SIGNALING PROTEIN 03-SEP-19 6SQ2 TITLE STRUCTURE OF A PHOSPHOMIMETIC SWITCH 2 VARIANT OF RAB8A IN COMPLEX TITLE 2 WITH THE PHOSPHO-RAB BINDING DOMAIN OF RILPL2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-8A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ONCOGENE C-MEL; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RILP-LIKE PROTEIN 2; COMPND 9 CHAIN: D, E; COMPND 10 SYNONYM: RAB-INTERACTING LYSOSOMAL PROTEIN-LIKE 2,P40PHOX-BINDING COMPND 11 PROTEIN; COMPND 12 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: RILPL2, RLP2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAB8A GTPASES, EFFECTOR, RILP-LIKE PROTEIN 2, SIGNALING COMPLEX, KEYWDS 2 LRRK2 PROTEIN KINASE, CILIOGENESIS, PARKINSON'S DISEASE, SIGNALING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.R.KHAN,D.WASCHBUSCH REVDAT 1 30-SEP-20 6SQ2 0 JRNL AUTH A.R.KHAN,D.WASCHBUSCH JRNL TITL STRUCTURE OF A PHOSPHOMIMETIC SWITCH 2 VARIANT OF RAB8A IN JRNL TITL 2 COMPLEX WITH THE PHOSPHO-RAB BINDING DOMAIN OF RILPL2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 56711 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 5300 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 61.0670 - 5.2300 0.99 3506 165 0.1817 0.2518 REMARK 3 2 5.2300 - 4.1515 0.99 3467 198 0.1436 0.1530 REMARK 3 3 4.1515 - 3.6268 0.96 3358 192 0.1491 0.1472 REMARK 3 4 3.6268 - 3.2952 0.97 3408 214 0.1638 0.1791 REMARK 3 5 3.2952 - 3.0590 0.99 3478 181 0.1683 0.1554 REMARK 3 6 3.0590 - 2.8787 0.99 3503 171 0.1670 0.1790 REMARK 3 7 2.8787 - 2.7345 1.00 3527 167 0.1802 0.2102 REMARK 3 8 2.7345 - 2.6155 0.97 3441 165 0.1862 0.2157 REMARK 3 9 2.6155 - 2.5148 1.00 3518 185 0.1820 0.2058 REMARK 3 10 2.5148 - 2.4280 0.99 3435 198 0.1746 0.2152 REMARK 3 11 2.4280 - 2.3521 1.00 3536 187 0.1636 0.1630 REMARK 3 12 2.3521 - 2.2848 1.00 3478 217 0.1680 0.1826 REMARK 3 13 2.2848 - 2.2247 0.89 3143 159 0.2062 0.2137 REMARK 3 14 2.2247 - 2.1704 1.00 3504 173 0.1763 0.2286 REMARK 3 15 2.1704 - 2.1211 1.00 3549 199 0.1800 0.2378 REMARK 3 16 2.1211 - 2.0759 0.97 3354 187 0.1917 0.2579 REMARK 3 17 2.0759 - 2.0344 0.88 3166 149 0.2157 0.2227 REMARK 3 18 2.0344 - 1.9960 0.99 3442 198 0.1816 0.2142 REMARK 3 19 1.9960 - 1.9604 1.00 3538 167 0.1809 0.2208 REMARK 3 20 1.9604 - 1.9271 0.92 3294 157 0.2347 0.2870 REMARK 3 21 1.9271 - 1.8960 0.85 2974 157 0.2964 0.3545 REMARK 3 22 1.8960 - 1.8669 0.96 3362 198 0.2321 0.2368 REMARK 3 23 1.8669 - 1.8394 0.99 3478 199 0.1914 0.2067 REMARK 3 24 1.8394 - 1.8135 1.00 3497 202 0.1830 0.2038 REMARK 3 25 1.8135 - 1.7890 0.99 3493 201 0.1903 0.2142 REMARK 3 26 1.7890 - 1.7657 0.97 3439 174 0.2136 0.2277 REMARK 3 27 1.7657 - 1.7437 0.88 3026 192 0.2504 0.2885 REMARK 3 28 1.7437 - 1.7227 0.78 2763 147 0.3051 0.3181 REMARK 3 29 1.7227 - 1.7026 0.72 2544 121 0.3440 0.3825 REMARK 3 30 1.7026 - 1.6840 0.45 1594 80 0.3579 0.4077 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.96 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -9.1724 -65.9984 6.0629 REMARK 3 T TENSOR REMARK 3 T11: 0.0933 T22: 0.1247 REMARK 3 T33: 0.0871 T12: -0.0022 REMARK 3 T13: -0.0084 T23: -0.0177 REMARK 3 L TENSOR REMARK 3 L11: 0.1175 L22: 1.4283 REMARK 3 L33: 0.0961 L12: 0.0120 REMARK 3 L13: -0.0243 L23: -0.3497 REMARK 3 S TENSOR REMARK 3 S11: -0.0149 S12: 0.0131 S13: 0.0116 REMARK 3 S21: 0.0093 S22: 0.0288 S23: -0.0380 REMARK 3 S31: 0.0055 S32: -0.0016 S33: -0.0031 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 6SQ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292104097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56711 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 61.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.40200 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: PHASER REMARK 200 STARTING MODEL: 4LHW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES 10% PEG 4,000 10% 2 REMARK 280 -PROPANOL, PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 30.34900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.19500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.86650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.19500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.34900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.86650 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 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: 6800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, E 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 178 REMARK 465 GLY A 179 REMARK 465 ASN A 180 REMARK 465 SER A 181 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 LYS B 3 REMARK 465 LEU B 177 REMARK 465 GLU B 178 REMARK 465 GLY B 179 REMARK 465 ASN B 180 REMARK 465 SER B 181 REMARK 465 HIS D 123 REMARK 465 HIS D 124 REMARK 465 HIS D 125 REMARK 465 HIS D 126 REMARK 465 HIS D 127 REMARK 465 HIS D 128 REMARK 465 GLN D 160 REMARK 465 CYS D 161 REMARK 465 TYR D 162 REMARK 465 LYS D 163 REMARK 465 SER D 164 REMARK 465 GLY D 165 REMARK 465 HIS E 123 REMARK 465 HIS E 124 REMARK 465 HIS E 125 REMARK 465 HIS E 126 REMARK 465 HIS E 127 REMARK 465 HIS E 128 REMARK 465 CYS E 161 REMARK 465 TYR E 162 REMARK 465 LYS E 163 REMARK 465 SER E 164 REMARK 465 GLY E 165 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 HOH B 1071 O HOH B 1157 1.86 REMARK 500 O HOH E 227 O HOH E 231 1.89 REMARK 500 O HOH A 1063 O HOH A 1112 1.94 REMARK 500 O HOH A 1046 O HOH A 1168 2.00 REMARK 500 O HOH A 1215 O HOH D 229 2.01 REMARK 500 O GLU E 158 N GLN E 160 2.03 REMARK 500 O HOH B 1005 O HOH B 1093 2.03 REMARK 500 O HOH A 1009 O HOH A 1117 2.04 REMARK 500 OH TYR B 7 O HOH B 1001 2.07 REMARK 500 O HOH A 1132 O HOH A 1163 2.08 REMARK 500 O HOH B 1013 O HOH B 1102 2.14 REMARK 500 O VAL E 154 CG GLU E 157 2.15 REMARK 500 O HOH B 1069 O HOH B 1153 2.17 REMARK 500 O HOH A 1069 O HOH A 1207 2.17 REMARK 500 O HOH B 1166 O HOH B 1205 2.19 REMARK 500 NH2 ARG A 167 O HOH A 1001 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 1026 O HOH B 1033 4535 1.73 REMARK 500 O HOH A 1094 O HOH A 1163 4525 1.92 REMARK 500 O HOH A 1102 O HOH A 1201 4425 2.05 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 SER A 39 CA SER A 39 C 0.166 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 LYS A 122 35.91 72.15 REMARK 500 ASP B 53 55.56 31.71 REMARK 500 LYS B 122 34.28 72.07 REMARK 500 VAL B 125 56.90 -100.14 REMARK 500 LYS B 175 60.37 -103.18 REMARK 500 ARG D 132 -31.93 -139.13 REMARK 500 GLU D 158 4.68 -53.75 REMARK 500 GLU E 157 -34.34 -38.93 REMARK 500 GLU E 158 12.21 -50.17 REMARK 500 LEU E 159 64.79 -55.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 39 16.64 REMARK 500 SER A 39 17.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1220 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A1221 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A1222 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH B1223 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH B1224 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH B1225 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH B1226 DISTANCE = 7.50 ANGSTROMS 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 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 22 OG1 REMARK 620 2 THR A 40 OG1 86.6 REMARK 620 3 GTP A 900 O3G 175.9 89.3 REMARK 620 4 GTP A 900 O2B 92.1 178.3 92.0 REMARK 620 5 HOH A1022 O 88.8 88.5 91.1 90.4 REMARK 620 6 HOH A1052 O 86.5 90.8 93.6 90.2 175.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 22 OG1 REMARK 620 2 THR B 40 OG1 86.0 REMARK 620 3 GTP B 900 O3G 177.1 92.6 REMARK 620 4 GTP B 900 O2B 90.5 176.0 90.9 REMARK 620 5 HOH B1017 O 90.5 90.0 92.0 88.2 REMARK 620 6 HOH B1047 O 88.7 94.7 88.9 87.1 175.2 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 GTP A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP B 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 901 DBREF 6SQ2 A 1 181 UNP P61006 RAB8A_HUMAN 1 181 DBREF 6SQ2 B 1 181 UNP P61006 RAB8A_HUMAN 1 181 DBREF 6SQ2 D 129 165 UNP Q969X0 RIPL2_HUMAN 129 165 DBREF 6SQ2 E 129 165 UNP Q969X0 RIPL2_HUMAN 129 165 SEQADV 6SQ2 GLY A -2 UNP P61006 EXPRESSION TAG SEQADV 6SQ2 SER A -1 UNP P61006 EXPRESSION TAG SEQADV 6SQ2 HIS A 0 UNP P61006 EXPRESSION TAG SEQADV 6SQ2 LEU A 67 UNP P61006 GLN 67 ENGINEERED MUTATION SEQADV 6SQ2 GLU A 72 UNP P61006 THR 72 ENGINEERED MUTATION SEQADV 6SQ2 GLY B -2 UNP P61006 EXPRESSION TAG SEQADV 6SQ2 SER B -1 UNP P61006 EXPRESSION TAG SEQADV 6SQ2 HIS B 0 UNP P61006 EXPRESSION TAG SEQADV 6SQ2 LEU B 67 UNP P61006 GLN 67 ENGINEERED MUTATION SEQADV 6SQ2 GLU B 72 UNP P61006 THR 72 ENGINEERED MUTATION SEQADV 6SQ2 HIS D 123 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS D 124 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS D 125 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS D 126 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS D 127 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS D 128 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS E 123 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS E 124 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS E 125 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS E 126 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS E 127 UNP Q969X0 EXPRESSION TAG SEQADV 6SQ2 HIS E 128 UNP Q969X0 EXPRESSION TAG SEQRES 1 A 184 GLY SER HIS MET ALA LYS THR TYR ASP TYR LEU PHE LYS SEQRES 2 A 184 LEU LEU LEU ILE GLY ASP SER GLY VAL GLY LYS THR CYS SEQRES 3 A 184 VAL LEU PHE ARG PHE SER GLU ASP ALA PHE ASN SER THR SEQRES 4 A 184 PHE ILE SER THR ILE GLY ILE ASP PHE LYS ILE ARG THR SEQRES 5 A 184 ILE GLU LEU ASP GLY LYS ARG ILE LYS LEU GLN ILE TRP SEQRES 6 A 184 ASP THR ALA GLY LEU GLU ARG PHE ARG GLU ILE THR THR SEQRES 7 A 184 ALA TYR TYR ARG GLY ALA MET GLY ILE MET LEU VAL TYR SEQRES 8 A 184 ASP ILE THR ASN GLU LYS SER PHE ASP ASN ILE ARG ASN SEQRES 9 A 184 TRP ILE ARG ASN ILE GLU GLU HIS ALA SER ALA ASP VAL SEQRES 10 A 184 GLU LYS MET ILE LEU GLY ASN LYS CYS ASP VAL ASN ASP SEQRES 11 A 184 LYS ARG GLN VAL SER LYS GLU ARG GLY GLU LYS LEU ALA SEQRES 12 A 184 LEU ASP TYR GLY ILE LYS PHE MET GLU THR SER ALA LYS SEQRES 13 A 184 ALA ASN ILE ASN VAL GLU ASN ALA PHE PHE THR LEU ALA SEQRES 14 A 184 ARG ASP ILE LYS ALA LYS MET ASP LYS LYS LEU GLU GLY SEQRES 15 A 184 ASN SER SEQRES 1 B 184 GLY SER HIS MET ALA LYS THR TYR ASP TYR LEU PHE LYS SEQRES 2 B 184 LEU LEU LEU ILE GLY ASP SER GLY VAL GLY LYS THR CYS SEQRES 3 B 184 VAL LEU PHE ARG PHE SER GLU ASP ALA PHE ASN SER THR SEQRES 4 B 184 PHE ILE SER THR ILE GLY ILE ASP PHE LYS ILE ARG THR SEQRES 5 B 184 ILE GLU LEU ASP GLY LYS ARG ILE LYS LEU GLN ILE TRP SEQRES 6 B 184 ASP THR ALA GLY LEU GLU ARG PHE ARG GLU ILE THR THR SEQRES 7 B 184 ALA TYR TYR ARG GLY ALA MET GLY ILE MET LEU VAL TYR SEQRES 8 B 184 ASP ILE THR ASN GLU LYS SER PHE ASP ASN ILE ARG ASN SEQRES 9 B 184 TRP ILE ARG ASN ILE GLU GLU HIS ALA SER ALA ASP VAL SEQRES 10 B 184 GLU LYS MET ILE LEU GLY ASN LYS CYS ASP VAL ASN ASP SEQRES 11 B 184 LYS ARG GLN VAL SER LYS GLU ARG GLY GLU LYS LEU ALA SEQRES 12 B 184 LEU ASP TYR GLY ILE LYS PHE MET GLU THR SER ALA LYS SEQRES 13 B 184 ALA ASN ILE ASN VAL GLU ASN ALA PHE PHE THR LEU ALA SEQRES 14 B 184 ARG ASP ILE LYS ALA LYS MET ASP LYS LYS LEU GLU GLY SEQRES 15 B 184 ASN SER SEQRES 1 D 43 HIS HIS HIS HIS HIS HIS ASN ARG PRO ARG PHE THR LEU SEQRES 2 D 43 GLN GLU LEU ARG ASP VAL LEU GLN GLU ARG ASN LYS LEU SEQRES 3 D 43 LYS SER GLN LEU LEU VAL VAL GLN GLU GLU LEU GLN CYS SEQRES 4 D 43 TYR LYS SER GLY SEQRES 1 E 43 HIS HIS HIS HIS HIS HIS ASN ARG PRO ARG PHE THR LEU SEQRES 2 E 43 GLN GLU LEU ARG ASP VAL LEU GLN GLU ARG ASN LYS LEU SEQRES 3 E 43 LYS SER GLN LEU LEU VAL VAL GLN GLU GLU LEU GLN CYS SEQRES 4 E 43 TYR LYS SER GLY HET GTP A 900 32 HET MG A 901 1 HET GTP B 900 32 HET MG B 901 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 5 GTP 2(C10 H16 N5 O14 P3) FORMUL 6 MG 2(MG 2+) FORMUL 9 HOH *513(H2 O) HELIX 1 AA1 GLY A 20 ASP A 31 1 12 HELIX 2 AA2 LEU A 67 ARG A 69 5 3 HELIX 3 AA3 PHE A 70 THR A 75 1 6 HELIX 4 AA4 ALA A 76 TYR A 78 5 3 HELIX 5 AA5 ASN A 92 ASN A 98 1 7 HELIX 6 AA6 ASN A 98 ALA A 110 1 13 HELIX 7 AA7 SER A 132 GLY A 144 1 13 HELIX 8 AA8 ASN A 157 LYS A 176 1 20 HELIX 9 AA9 GLY B 20 ASP B 31 1 12 HELIX 10 AB1 LEU B 67 ARG B 69 5 3 HELIX 11 AB2 PHE B 70 ALA B 76 1 7 HELIX 12 AB3 ASN B 92 ASN B 98 1 7 HELIX 13 AB4 ASN B 98 ALA B 110 1 13 HELIX 14 AB5 VAL B 125 ARG B 129 5 5 HELIX 15 AB6 SER B 132 GLY B 144 1 13 HELIX 16 AB7 ASN B 157 LYS B 175 1 19 HELIX 17 AB8 THR D 134 GLU D 158 1 25 HELIX 18 AB9 THR E 134 GLU E 157 1 24 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 57 N ILE A 50 SHEET 3 AA1 6 TYR A 7 ILE A 14 1 N LEU A 11 O TRP A 62 SHEET 4 AA1 6 GLY A 83 ASP A 89 1 O MET A 85 N LEU A 12 SHEET 5 AA1 6 GLU A 115 ASN A 121 1 O MET A 117 N LEU A 86 SHEET 6 AA1 6 LYS A 146 GLU A 149 1 O LYS A 146 N ILE A 118 SHEET 1 AA2 6 ILE B 43 LEU B 52 0 SHEET 2 AA2 6 LYS B 55 THR B 64 -1 O LYS B 55 N LEU B 52 SHEET 3 AA2 6 TYR B 7 ILE B 14 1 N LEU B 11 O TRP B 62 SHEET 4 AA2 6 GLY B 83 ASP B 89 1 O MET B 85 N LEU B 12 SHEET 5 AA2 6 GLU B 115 ASN B 121 1 O MET B 117 N LEU B 86 SHEET 6 AA2 6 LYS B 146 GLU B 149 1 O LYS B 146 N ILE B 118 LINK OG1 THR A 22 MG MG A 901 1555 1555 2.12 LINK OG1 THR A 40 MG MG A 901 1555 1555 2.19 LINK O3G GTP A 900 MG MG A 901 1555 1555 2.06 LINK O2B GTP A 900 MG MG A 901 1555 1555 2.04 LINK MG MG A 901 O HOH A1022 1555 1555 2.14 LINK MG MG A 901 O HOH A1052 1555 1555 2.21 LINK OG1 THR B 22 MG MG B 901 1555 1555 2.03 LINK OG1 THR B 40 MG MG B 901 1555 1555 2.11 LINK O3G GTP B 900 MG MG B 901 1555 1555 2.07 LINK O2B GTP B 900 MG MG B 901 1555 1555 2.06 LINK MG MG B 901 O HOH B1017 1555 1555 2.13 LINK MG MG B 901 O HOH B1047 1555 1555 2.13 SITE 1 AC1 26 SER A 17 GLY A 18 VAL A 19 GLY A 20 SITE 2 AC1 26 LYS A 21 THR A 22 CYS A 23 PHE A 33 SITE 3 AC1 26 SER A 35 PHE A 37 SER A 39 THR A 40 SITE 4 AC1 26 GLY A 66 ASN A 121 LYS A 122 ASP A 124 SITE 5 AC1 26 SER A 151 ALA A 152 LYS A 153 MG A 901 SITE 6 AC1 26 HOH A1003 HOH A1022 HOH A1044 HOH A1052 SITE 7 AC1 26 HOH A1074 HOH A1101 SITE 1 AC2 5 THR A 22 THR A 40 GTP A 900 HOH A1022 SITE 2 AC2 5 HOH A1052 SITE 1 AC3 29 SER B 17 GLY B 18 VAL B 19 GLY B 20 SITE 2 AC3 29 LYS B 21 THR B 22 CYS B 23 PHE B 33 SITE 3 AC3 29 ASN B 34 SER B 35 PHE B 37 SER B 39 SITE 4 AC3 29 THR B 40 GLY B 66 ASN B 121 LYS B 122 SITE 5 AC3 29 ASP B 124 VAL B 125 SER B 151 ALA B 152 SITE 6 AC3 29 LYS B 153 MG B 901 HOH B1017 HOH B1047 SITE 7 AC3 29 HOH B1050 HOH B1064 HOH B1120 HOH B1126 SITE 8 AC3 29 HOH B1132 SITE 1 AC4 5 THR B 22 THR B 40 GTP B 900 HOH B1017 SITE 2 AC4 5 HOH B1047 CRYST1 60.698 71.733 116.390 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 0.016475 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008592 0.00000