HEADER HYDROLASE 06-DEC-05 2F9L TITLE 3D STRUCTURE OF INACTIVE HUMAN RAB11B GTPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAB11B, MEMBER RAS ONCOGENE FAMILY; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GTPASE DOMAIN, RESIDUES 8 TO 205; COMPND 5 EC: 3.6.5.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCYTEXP3 KEYWDS RAB11B GTPASE, VESICLE TRANSPORT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.M.N.SCAPIN,B.G.GUIMARAES,N.I.T.ZANCHIN REVDAT 5 30-AUG-23 2F9L 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2F9L 1 REMARK REVDAT 3 24-FEB-09 2F9L 1 VERSN REVDAT 2 30-MAY-06 2F9L 1 JRNL REVDAT 1 04-APR-06 2F9L 0 JRNL AUTH S.M.SCAPIN,F.R.CARNEIRO,A.C.ALVES,F.J.MEDRANO,B.G.GUIMARAES, JRNL AUTH 2 N.I.ZANCHIN JRNL TITL THE CRYSTAL STRUCTURE OF THE SMALL GTPASE RAB11B REVEALS JRNL TITL 2 CRITICAL DIFFERENCES RELATIVE TO THE RAB11A ISOFORM. JRNL REF J.STRUCT.BIOL. V. 154 260 2006 JRNL REFN ISSN 1047-8477 JRNL PMID 16545962 JRNL DOI 10.1016/J.JSB.2006.01.007 REMARK 2 REMARK 2 RESOLUTION. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 20119 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1091 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1434 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1341 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 185 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.34000 REMARK 3 B22 (A**2) : -0.70000 REMARK 3 B33 (A**2) : 1.04000 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): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.734 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1391 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1892 ; 1.720 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 171 ; 5.909 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;37.806 ;24.531 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 226 ;16.101 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;23.694 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 220 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1033 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 824 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1001 ; 0.332 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 203 ; 0.152 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 88 ; 0.211 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 42 ; 0.190 ; 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): 862 ; 0.975 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1362 ; 1.631 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 601 ; 2.400 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 530 ; 3.464 ; 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 : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 2F9L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000035622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : D03B-MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.43 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21134 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 39.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37700 REMARK 200 FOR SHELL : 5.000 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: PDB ENTRY 1OIV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 22.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION: 0.1M TRIS-HCL REMARK 280 PH8.8, 30% PEG 4000 PROTEIN SAMPLE: 30 MG/ML RAB11B-GDP, 10MM REMARK 280 TRIS-HCL PH7.4, 0.1MM MG CHLORIDE , VAPOR DIFFUSION, HANGING REMARK 280 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 22.89500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.67550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.10900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.67550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.89500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.10900 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLU A 39 REMARK 465 SER A 40 REMARK 465 LYS A 41 REMARK 465 ASP A 183 REMARK 465 ARG A 184 REMARK 465 ALA A 185 REMARK 465 ALA A 186 REMARK 465 HIS A 187 REMARK 465 ASP A 188 REMARK 465 GLU A 189 REMARK 465 SER A 190 REMARK 465 PRO A 191 REMARK 465 GLY A 192 REMARK 465 ASN A 193 REMARK 465 ASN A 194 REMARK 465 VAL A 195 REMARK 465 VAL A 196 REMARK 465 ASP A 197 REMARK 465 ILE A 198 REMARK 465 SER A 199 REMARK 465 VAL A 200 REMARK 465 PRO A 201 REMARK 465 PRO A 202 REMARK 465 THR A 203 REMARK 465 THR A 204 REMARK 465 ASP A 205 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 MET A 7 CB CG SD CE REMARK 470 SER A 42 OG REMARK 470 ARG A 74 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 82 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 104 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 ARG A 110 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 112 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 115 OG REMARK 470 LYS A 145 CG CD CE NZ 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 C ASP A 114 O HOH A 1357 2.00 REMARK 500 O HOH A 1328 O HOH A 1353 2.13 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 CB ARG A 82 O HOH A 1358 4556 2.04 REMARK 500 O HOH A 1328 O HOH A 1355 4555 2.19 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 MET A 120 CG - SD - CE ANGL. DEV. = -16.5 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 ARG A 74 32.70 79.58 REMARK 500 LEU A 109 -80.29 -64.26 REMARK 500 ARG A 110 -43.58 -26.95 REMARK 500 ASP A 111 -75.49 -68.39 REMARK 500 SER A 115 -35.21 -31.42 REMARK 500 LYS A 125 37.29 72.49 REMARK 500 SER A 158 -3.05 74.68 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 A1175 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 25 OG REMARK 620 2 GDP A1174 O3B 87.7 REMARK 620 3 HOH A1296 O 93.9 89.8 REMARK 620 4 HOH A1297 O 85.7 173.2 89.1 REMARK 620 5 HOH A1298 O 88.2 93.1 176.5 88.3 REMARK 620 6 HOH A1299 O 174.5 92.3 91.6 94.4 86.2 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 MG A 1175 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 1174 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2F9M RELATED DB: PDB REMARK 900 3D STRUCTURE OF ACTIVE HUMAN RAB11B GTPASE DBREF 2F9L A 8 205 UNP Q15907 RB11B_HUMAN 8 205 SEQADV 2F9L MET A 7 UNP Q15907 INITIATING METHIONINE SEQRES 1 A 199 MET TYR ASP TYR LEU PHE LYS VAL VAL LEU ILE GLY ASP SEQRES 2 A 199 SER GLY VAL GLY LYS SER ASN LEU LEU SER ARG PHE THR SEQRES 3 A 199 ARG ASN GLU PHE ASN LEU GLU SER LYS SER THR ILE GLY SEQRES 4 A 199 VAL GLU PHE ALA THR ARG SER ILE GLN VAL ASP GLY LYS SEQRES 5 A 199 THR ILE LYS ALA GLN ILE TRP ASP THR ALA GLY GLN GLU SEQRES 6 A 199 ARG TYR ARG ARG ILE THR SER ALA TYR TYR ARG GLY ALA SEQRES 7 A 199 VAL GLY ALA LEU LEU VAL TYR ASP ILE ALA LYS HIS LEU SEQRES 8 A 199 THR TYR GLU ASN VAL GLU ARG TRP LEU LYS GLU LEU ARG SEQRES 9 A 199 ASP HIS ALA ASP SER ASN ILE VAL ILE MET LEU VAL GLY SEQRES 10 A 199 ASN LYS SER ASP LEU ARG HIS LEU ARG ALA VAL PRO THR SEQRES 11 A 199 ASP GLU ALA ARG ALA PHE ALA GLU LYS ASN ASN LEU SER SEQRES 12 A 199 PHE ILE GLU THR SER ALA LEU ASP SER THR ASN VAL GLU SEQRES 13 A 199 GLU ALA PHE LYS ASN ILE LEU THR GLU ILE TYR ARG ILE SEQRES 14 A 199 VAL SER GLN LYS GLN ILE ALA ASP ARG ALA ALA HIS ASP SEQRES 15 A 199 GLU SER PRO GLY ASN ASN VAL VAL ASP ILE SER VAL PRO SEQRES 16 A 199 PRO THR THR ASP HET MG A1175 1 HET GDP A1174 28 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 HOH *185(H2 O) HELIX 1 1 GLY A 23 ASN A 34 1 12 HELIX 2 2 GLY A 69 TYR A 73 5 5 HELIX 3 3 THR A 77 ARG A 82 1 6 HELIX 4 4 LYS A 95 ASN A 101 1 7 HELIX 5 5 ASN A 101 ALA A 113 1 13 HELIX 6 6 LEU A 128 ARG A 132 5 5 HELIX 7 7 PRO A 135 ASN A 146 1 12 HELIX 8 8 ASN A 160 GLN A 178 1 19 SHEET 1 A 6 GLU A 47 VAL A 55 0 SHEET 2 A 6 LYS A 58 ASP A 66 -1 O ILE A 60 N ILE A 53 SHEET 3 A 6 TYR A 10 ILE A 17 1 N TYR A 10 O LYS A 61 SHEET 4 A 6 GLY A 86 ASP A 92 1 O VAL A 90 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 LINK OG SER A 25 MG MG A1175 1555 1555 2.13 LINK O3B GDP A1174 MG MG A1175 1555 1555 2.01 LINK MG MG A1175 O HOH A1296 1555 1555 2.04 LINK MG MG A1175 O HOH A1297 1555 1555 2.05 LINK MG MG A1175 O HOH A1298 1555 1555 2.14 LINK MG MG A1175 O HOH A1299 1555 1555 2.08 SITE 1 AC1 6 SER A 25 GDP A1174 HOH A1296 HOH A1297 SITE 2 AC1 6 HOH A1298 HOH A1299 SITE 1 AC2 25 GLY A 21 VAL A 22 GLY A 23 LYS A 24 SITE 2 AC2 25 SER A 25 ASN A 26 PHE A 36 ASN A 37 SITE 3 AC2 25 LEU A 38 ASN A 124 LYS A 125 ASP A 127 SITE 4 AC2 25 SER A 154 ALA A 155 LEU A 156 MG A1175 SITE 5 AC2 25 HOH A1190 HOH A1201 HOH A1216 HOH A1222 SITE 6 AC2 25 HOH A1240 HOH A1241 HOH A1296 HOH A1298 SITE 7 AC2 25 HOH A1299 CRYST1 45.790 52.218 59.351 90.00 90.00 90.00 P 21 21 21 4 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 0.021839 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016849 0.00000