HEADER PROTEIN TRANSPORT 03-FEB-21 7E1T TITLE CRYSTAL STRUCTURE OF RAB9A-GTP-NDE1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-9A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: GTPASE DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ISOFORM 2 OF NUCLEAR DISTRIBUTION PROTEIN NUDE HOMOLOG 1; COMPND 9 CHAIN: C, D; COMPND 10 SYNONYM: NUDE; COMPND 11 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: RAB9A, RAB9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM30; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: NDE1, NUDE; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS RAB9A, NDE1, RAB GTPASE, EFFECTOR, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHANG,T.ZHANG,J.DING REVDAT 3 29-NOV-23 7E1T 1 REMARK REVDAT 2 18-MAY-22 7E1T 1 JRNL REVDAT 1 27-OCT-21 7E1T 0 JRNL AUTH Y.ZHANG,Z.CHEN,F.WANG,H.SUN,X.ZHU,J.DING,T.ZHANG JRNL TITL NDE1 IS A RAB9 EFFECTOR FOR LOADING LATE ENDOSOMES TO JRNL TITL 2 CYTOPLASMIC DYNEIN MOTOR COMPLEX. JRNL REF STRUCTURE V. 30 386 2022 JRNL REFN ISSN 0969-2126 JRNL PMID 34793709 JRNL DOI 10.1016/J.STR.2021.10.013 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0123 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 3 NUMBER OF REFLECTIONS : 17293 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 926 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 944 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3220 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.98000 REMARK 3 B22 (A**2) : -1.18000 REMARK 3 B33 (A**2) : 0.19000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.283 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.217 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.188 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3359 ; 0.008 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4554 ; 1.202 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 5.819 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;36.934 ;24.368 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 563 ;17.875 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;19.965 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 493 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2555 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 3266 ;16.971 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3203 ;24.257 ; 5.000 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 175 REMARK 3 ORIGIN FOR THE GROUP (A): 2.8189 -19.5085 -7.5905 REMARK 3 T TENSOR REMARK 3 T11: 0.0016 T22: 0.0952 REMARK 3 T33: 0.0348 T12: -0.0010 REMARK 3 T13: 0.0025 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.0274 L22: 0.0707 REMARK 3 L33: 0.1587 L12: -0.0288 REMARK 3 L13: 0.0389 L23: -0.1045 REMARK 3 S TENSOR REMARK 3 S11: 0.0047 S12: -0.0134 S13: 0.0038 REMARK 3 S21: -0.0017 S22: 0.0018 S23: -0.0028 REMARK 3 S31: 0.0007 S32: -0.0096 S33: -0.0065 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 179 REMARK 3 ORIGIN FOR THE GROUP (A): 17.5434 -50.1639 22.9387 REMARK 3 T TENSOR REMARK 3 T11: 0.0152 T22: 0.0931 REMARK 3 T33: 0.0156 T12: 0.0070 REMARK 3 T13: -0.0016 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.3166 L22: 0.0859 REMARK 3 L33: 0.2987 L12: 0.1124 REMARK 3 L13: 0.0457 L23: -0.0089 REMARK 3 S TENSOR REMARK 3 S11: 0.0101 S12: 0.0087 S13: -0.0012 REMARK 3 S21: -0.0070 S22: 0.0090 S23: -0.0112 REMARK 3 S31: 0.0334 S32: 0.0102 S33: -0.0191 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 98 C 130 REMARK 3 ORIGIN FOR THE GROUP (A): 1.5847 -41.7689 3.2712 REMARK 3 T TENSOR REMARK 3 T11: 0.0023 T22: 0.1080 REMARK 3 T33: 0.0549 T12: -0.0052 REMARK 3 T13: 0.0028 T23: 0.0113 REMARK 3 L TENSOR REMARK 3 L11: 0.0071 L22: 0.0337 REMARK 3 L33: 0.2157 L12: -0.0152 REMARK 3 L13: -0.0365 L23: 0.0748 REMARK 3 S TENSOR REMARK 3 S11: 0.0028 S12: 0.0066 S13: 0.0032 REMARK 3 S21: -0.0067 S22: -0.0231 S23: -0.0128 REMARK 3 S31: -0.0157 S32: -0.0373 S33: 0.0203 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 97 D 121 REMARK 3 ORIGIN FOR THE GROUP (A): 5.1228 -33.0733 11.4770 REMARK 3 T TENSOR REMARK 3 T11: 0.0102 T22: 0.1229 REMARK 3 T33: 0.0372 T12: -0.0121 REMARK 3 T13: -0.0045 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.1554 L22: 0.1820 REMARK 3 L33: 0.0131 L12: -0.1681 REMARK 3 L13: 0.0451 L23: -0.0488 REMARK 3 S TENSOR REMARK 3 S11: -0.0324 S12: -0.0210 S13: 0.0180 REMARK 3 S21: 0.0378 S22: 0.0248 S23: -0.0171 REMARK 3 S31: -0.0101 S32: -0.0059 S33: 0.0076 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: U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 7E1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1300020629. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18238 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 47.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4QXA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 5.5 AND 25% PEG REMARK 280 3350., EVAPORATION, TEMPERATURE 290K 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 33.71050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.25800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.82300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.25800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.71050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.82300 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: 5860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 ALA A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 LYS A 4 REMARK 465 SER A 5 REMARK 465 GLU A 176 REMARK 465 ASP A 177 REMARK 465 ARG A 178 REMARK 465 SER A 179 REMARK 465 ASP A 180 REMARK 465 HIS A 181 REMARK 465 LEU A 182 REMARK 465 ILE A 183 REMARK 465 GLN A 184 REMARK 465 THR A 185 REMARK 465 ASP A 186 REMARK 465 THR A 187 REMARK 465 VAL A 188 REMARK 465 ASN A 189 REMARK 465 LEU A 190 REMARK 465 HIS A 191 REMARK 465 ARG A 192 REMARK 465 LYS A 193 REMARK 465 PRO A 194 REMARK 465 LYS A 195 REMARK 465 PRO A 196 REMARK 465 SER A 197 REMARK 465 SER A 198 REMARK 465 SER A 199 REMARK 465 CYS A 200 REMARK 465 CYS A 201 REMARK 465 GLY B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLY B 3 REMARK 465 LYS B 4 REMARK 465 SER B 5 REMARK 465 ASP B 180 REMARK 465 HIS B 181 REMARK 465 LEU B 182 REMARK 465 ILE B 183 REMARK 465 GLN B 184 REMARK 465 THR B 185 REMARK 465 ASP B 186 REMARK 465 THR B 187 REMARK 465 VAL B 188 REMARK 465 ASN B 189 REMARK 465 LEU B 190 REMARK 465 HIS B 191 REMARK 465 ARG B 192 REMARK 465 LYS B 193 REMARK 465 PRO B 194 REMARK 465 LYS B 195 REMARK 465 PRO B 196 REMARK 465 SER B 197 REMARK 465 SER B 198 REMARK 465 SER B 199 REMARK 465 CYS B 200 REMARK 465 CYS B 201 REMARK 465 MET C 97 REMARK 465 THR C 131 REMARK 465 ILE C 132 REMARK 465 MET C 133 REMARK 465 SER C 134 REMARK 465 LEU C 135 REMARK 465 GLU C 136 REMARK 465 ASP C 137 REMARK 465 PHE C 138 REMARK 465 GLU C 139 REMARK 465 GLN C 140 REMARK 465 ARG C 141 REMARK 465 LEU C 142 REMARK 465 ASN C 143 REMARK 465 GLN C 144 REMARK 465 ALA C 145 REMARK 465 ILE C 146 REMARK 465 GLU C 147 REMARK 465 ARG C 148 REMARK 465 ASN C 149 REMARK 465 ALA C 150 REMARK 465 PHE C 151 REMARK 465 LEU C 152 REMARK 465 GLU C 153 REMARK 465 SER C 154 REMARK 465 GLU C 155 REMARK 465 LEU C 156 REMARK 465 ASP C 157 REMARK 465 GLU C 158 REMARK 465 LYS C 159 REMARK 465 GLU C 160 REMARK 465 ASN C 161 REMARK 465 LEU C 162 REMARK 465 LEU C 163 REMARK 465 GLU C 164 REMARK 465 SER C 165 REMARK 465 VAL C 166 REMARK 465 GLN C 167 REMARK 465 ARG C 168 REMARK 465 ASP D 122 REMARK 465 ASP D 123 REMARK 465 LEU D 124 REMARK 465 GLU D 125 REMARK 465 ARG D 126 REMARK 465 ALA D 127 REMARK 465 LYS D 128 REMARK 465 ARG D 129 REMARK 465 ALA D 130 REMARK 465 THR D 131 REMARK 465 ILE D 132 REMARK 465 MET D 133 REMARK 465 SER D 134 REMARK 465 LEU D 135 REMARK 465 GLU D 136 REMARK 465 ASP D 137 REMARK 465 PHE D 138 REMARK 465 GLU D 139 REMARK 465 GLN D 140 REMARK 465 ARG D 141 REMARK 465 LEU D 142 REMARK 465 ASN D 143 REMARK 465 GLN D 144 REMARK 465 ALA D 145 REMARK 465 ILE D 146 REMARK 465 GLU D 147 REMARK 465 ARG D 148 REMARK 465 ASN D 149 REMARK 465 ALA D 150 REMARK 465 PHE D 151 REMARK 465 LEU D 152 REMARK 465 GLU D 153 REMARK 465 SER D 154 REMARK 465 GLU D 155 REMARK 465 LEU D 156 REMARK 465 ASP D 157 REMARK 465 GLU D 158 REMARK 465 LYS D 159 REMARK 465 GLU D 160 REMARK 465 ASN D 161 REMARK 465 LEU D 162 REMARK 465 LEU D 163 REMARK 465 GLU D 164 REMARK 465 SER D 165 REMARK 465 VAL D 166 REMARK 465 GLN D 167 REMARK 465 ARG D 168 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 112 CG CD CE NZ REMARK 470 THR A 175 OG1 CG2 REMARK 470 LYS B 103 CG CD CE NZ REMARK 470 GLU B 115 CG CD OE1 OE2 REMARK 470 GLU B 130 CG CD OE1 OE2 REMARK 470 ASP B 177 CG OD1 OD2 REMARK 470 ARG B 178 CG CD NE CZ NH1 NH2 REMARK 470 ASN D 121 CG OD1 ND2 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 GLN A 35 70.70 -117.80 REMARK 500 GLN B 35 45.53 -95.12 REMARK 500 ALA B 158 -0.31 79.32 REMARK 500 ASN B 160 11.56 58.40 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 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 21 OG REMARK 620 2 THR A 39 OG1 81.3 REMARK 620 3 GTP A 302 O3G 177.9 100.8 REMARK 620 4 GTP A 302 O2B 104.3 172.5 73.6 REMARK 620 5 HOH A 406 O 89.9 87.6 90.6 87.4 REMARK 620 6 HOH A 415 O 98.3 101.4 81.0 82.9 168.6 REMARK 620 N 1 2 3 4 5 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 21 OG REMARK 620 2 THR B 39 OG1 75.4 REMARK 620 3 GTP B 302 O3G 169.2 100.5 REMARK 620 4 GTP B 302 O1B 109.2 175.4 75.0 REMARK 620 5 HOH B 401 O 106.6 93.6 83.5 85.1 REMARK 620 6 HOH B 411 O 82.2 88.1 87.7 92.5 171.2 REMARK 620 N 1 2 3 4 5 DBREF 7E1T A 1 201 UNP P51151 RAB9A_HUMAN 1 201 DBREF 7E1T B 1 201 UNP P51151 RAB9A_HUMAN 1 201 DBREF 7E1T C 98 168 UNP Q9NXR1 NDE1_HUMAN 98 168 DBREF 7E1T D 98 168 UNP Q9NXR1 NDE1_HUMAN 98 168 SEQADV 7E1T GLY A -1 UNP P51151 EXPRESSION TAG SEQADV 7E1T ALA A 0 UNP P51151 EXPRESSION TAG SEQADV 7E1T LEU A 66 UNP P51151 GLN 66 ENGINEERED MUTATION SEQADV 7E1T GLY B -1 UNP P51151 EXPRESSION TAG SEQADV 7E1T ALA B 0 UNP P51151 EXPRESSION TAG SEQADV 7E1T LEU B 66 UNP P51151 GLN 66 ENGINEERED MUTATION SEQADV 7E1T MET C 97 UNP Q9NXR1 INITIATING METHIONINE SEQADV 7E1T MET D 97 UNP Q9NXR1 INITIATING METHIONINE SEQRES 1 A 203 GLY ALA MET ALA GLY LYS SER SER LEU PHE LYS VAL ILE SEQRES 2 A 203 LEU LEU GLY ASP GLY GLY VAL GLY LYS SER SER LEU MET SEQRES 3 A 203 ASN ARG TYR VAL THR ASN LYS PHE ASP THR GLN LEU PHE SEQRES 4 A 203 HIS THR ILE GLY VAL GLU PHE LEU ASN LYS ASP LEU GLU SEQRES 5 A 203 VAL ASP GLY HIS PHE VAL THR MET GLN ILE TRP ASP THR SEQRES 6 A 203 ALA GLY LEU GLU ARG PHE ARG SER LEU ARG THR PRO PHE SEQRES 7 A 203 TYR ARG GLY SER ASP CYS CYS LEU LEU THR PHE SER VAL SEQRES 8 A 203 ASP ASP SER GLN SER PHE GLN ASN LEU SER ASN TRP LYS SEQRES 9 A 203 LYS GLU PHE ILE TYR TYR ALA ASP VAL LYS GLU PRO GLU SEQRES 10 A 203 SER PHE PRO PHE VAL ILE LEU GLY ASN LYS ILE ASP ILE SEQRES 11 A 203 SER GLU ARG GLN VAL SER THR GLU GLU ALA GLN ALA TRP SEQRES 12 A 203 CYS ARG ASP ASN GLY ASP TYR PRO TYR PHE GLU THR SER SEQRES 13 A 203 ALA LYS ASP ALA THR ASN VAL ALA ALA ALA PHE GLU GLU SEQRES 14 A 203 ALA VAL ARG ARG VAL LEU ALA THR GLU ASP ARG SER ASP SEQRES 15 A 203 HIS LEU ILE GLN THR ASP THR VAL ASN LEU HIS ARG LYS SEQRES 16 A 203 PRO LYS PRO SER SER SER CYS CYS SEQRES 1 B 203 GLY ALA MET ALA GLY LYS SER SER LEU PHE LYS VAL ILE SEQRES 2 B 203 LEU LEU GLY ASP GLY GLY VAL GLY LYS SER SER LEU MET SEQRES 3 B 203 ASN ARG TYR VAL THR ASN LYS PHE ASP THR GLN LEU PHE SEQRES 4 B 203 HIS THR ILE GLY VAL GLU PHE LEU ASN LYS ASP LEU GLU SEQRES 5 B 203 VAL ASP GLY HIS PHE VAL THR MET GLN ILE TRP ASP THR SEQRES 6 B 203 ALA GLY LEU GLU ARG PHE ARG SER LEU ARG THR PRO PHE SEQRES 7 B 203 TYR ARG GLY SER ASP CYS CYS LEU LEU THR PHE SER VAL SEQRES 8 B 203 ASP ASP SER GLN SER PHE GLN ASN LEU SER ASN TRP LYS SEQRES 9 B 203 LYS GLU PHE ILE TYR TYR ALA ASP VAL LYS GLU PRO GLU SEQRES 10 B 203 SER PHE PRO PHE VAL ILE LEU GLY ASN LYS ILE ASP ILE SEQRES 11 B 203 SER GLU ARG GLN VAL SER THR GLU GLU ALA GLN ALA TRP SEQRES 12 B 203 CYS ARG ASP ASN GLY ASP TYR PRO TYR PHE GLU THR SER SEQRES 13 B 203 ALA LYS ASP ALA THR ASN VAL ALA ALA ALA PHE GLU GLU SEQRES 14 B 203 ALA VAL ARG ARG VAL LEU ALA THR GLU ASP ARG SER ASP SEQRES 15 B 203 HIS LEU ILE GLN THR ASP THR VAL ASN LEU HIS ARG LYS SEQRES 16 B 203 PRO LYS PRO SER SER SER CYS CYS SEQRES 1 C 72 MET ASP ASP LEU ALA GLN THR LYS ALA ILE LYS ASP GLN SEQRES 2 C 72 LEU GLN LYS TYR ILE ARG GLU LEU GLU GLN ALA ASN ASP SEQRES 3 C 72 ASP LEU GLU ARG ALA LYS ARG ALA THR ILE MET SER LEU SEQRES 4 C 72 GLU ASP PHE GLU GLN ARG LEU ASN GLN ALA ILE GLU ARG SEQRES 5 C 72 ASN ALA PHE LEU GLU SER GLU LEU ASP GLU LYS GLU ASN SEQRES 6 C 72 LEU LEU GLU SER VAL GLN ARG SEQRES 1 D 72 MET ASP ASP LEU ALA GLN THR LYS ALA ILE LYS ASP GLN SEQRES 2 D 72 LEU GLN LYS TYR ILE ARG GLU LEU GLU GLN ALA ASN ASP SEQRES 3 D 72 ASP LEU GLU ARG ALA LYS ARG ALA THR ILE MET SER LEU SEQRES 4 D 72 GLU ASP PHE GLU GLN ARG LEU ASN GLN ALA ILE GLU ARG SEQRES 5 D 72 ASN ALA PHE LEU GLU SER GLU LEU ASP GLU LYS GLU ASN SEQRES 6 D 72 LEU LEU GLU SER VAL GLN ARG HET MG A 301 1 HET GTP A 302 32 HET MG B 301 1 HET GTP B 302 32 HETNAM MG MAGNESIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 5 MG 2(MG 2+) FORMUL 6 GTP 2(C10 H16 N5 O14 P3) FORMUL 9 HOH *153(H2 O) HELIX 1 AA1 GLY A 19 ASN A 30 1 12 HELIX 2 AA2 LEU A 66 ARG A 68 5 3 HELIX 3 AA3 PHE A 69 THR A 74 1 6 HELIX 4 AA4 PRO A 75 TYR A 77 5 3 HELIX 5 AA5 ASP A 91 ASN A 97 1 7 HELIX 6 AA6 ASN A 97 ASP A 110 1 14 HELIX 7 AA7 GLU A 113 PHE A 117 5 5 HELIX 8 AA8 SER A 134 ASP A 144 1 11 HELIX 9 AA9 ASN A 160 THR A 175 1 16 HELIX 10 AB1 GLY B 19 ASN B 30 1 12 HELIX 11 AB2 LEU B 66 ARG B 68 5 3 HELIX 12 AB3 PHE B 69 THR B 74 1 6 HELIX 13 AB4 PRO B 75 TYR B 77 5 3 HELIX 14 AB5 ASP B 91 ASN B 97 1 7 HELIX 15 AB6 ASN B 97 ALA B 109 1 13 HELIX 16 AB7 SER B 134 ASN B 145 1 12 HELIX 17 AB8 ASN B 160 ASP B 177 1 18 HELIX 18 AB9 ASP C 99 ALA C 130 1 32 HELIX 19 AC1 ASP D 98 ASN D 121 1 24 SHEET 1 AA1 6 VAL A 42 VAL A 51 0 SHEET 2 AA1 6 HIS A 54 THR A 63 -1 O HIS A 54 N VAL A 51 SHEET 3 AA1 6 LEU A 7 LEU A 13 1 N VAL A 10 O TRP A 61 SHEET 4 AA1 6 CYS A 82 SER A 88 1 O LEU A 84 N ILE A 11 SHEET 5 AA1 6 PHE A 119 ASN A 124 1 O ASN A 124 N PHE A 87 SHEET 6 AA1 6 TYR A 150 GLU A 152 1 O PHE A 151 N GLY A 123 SHEET 1 AA2 6 VAL B 42 VAL B 51 0 SHEET 2 AA2 6 HIS B 54 THR B 63 -1 O ASP B 62 N GLU B 43 SHEET 3 AA2 6 LEU B 7 GLY B 14 1 N VAL B 10 O TRP B 61 SHEET 4 AA2 6 CYS B 82 SER B 88 1 O LEU B 84 N ILE B 11 SHEET 5 AA2 6 PHE B 119 ASN B 124 1 O LEU B 122 N LEU B 85 SHEET 6 AA2 6 TYR B 150 GLU B 152 1 O PHE B 151 N ILE B 121 LINK OG SER A 21 MG MG A 301 1555 1555 2.24 LINK OG1 THR A 39 MG MG A 301 1555 1555 2.21 LINK MG MG A 301 O3G GTP A 302 1555 1555 2.28 LINK MG MG A 301 O2B GTP A 302 1555 1555 2.22 LINK MG MG A 301 O HOH A 406 1555 1555 2.48 LINK MG MG A 301 O HOH A 415 1555 1555 2.22 LINK OG SER B 21 MG MG B 301 1555 1555 2.27 LINK OG1 THR B 39 MG MG B 301 1555 1555 2.24 LINK MG MG B 301 O3G GTP B 302 1555 1555 2.25 LINK MG MG B 301 O1B GTP B 302 1555 1555 2.19 LINK MG MG B 301 O HOH B 401 1555 1555 2.21 LINK MG MG B 301 O HOH B 411 1555 1555 2.40 CRYST1 67.421 67.646 118.516 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 0.014832 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014783 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008438 0.00000