HEADER STRUCTURAL GENOMICS 01-JUL-19 6S5H TITLE STRUCTURE OF THE HUMAN RAB38 IN COMPLEX WITH GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-38; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MELANOMA ANTIGEN NY-MEL-1; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: RESIDUES NOT VISIBLE IN THE STRUCTURE: 135 TO 141 AND COMPND 7 185 TO END SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAB38; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GTPASE, RAS-RELATED PROTEIN RAB-38, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR L.DIAZ-SAEZ,S.JUNG,F.VON DELFT,C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA, AUTHOR 2 K.HUBER,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 24-JAN-24 6S5H 1 REMARK REVDAT 1 22-JUL-20 6S5H 0 JRNL AUTH L.DIAZ-SAEZ,S.A JUNG,K.HUBER,F.VON DELFT,C.H.ARROWSMITH, JRNL AUTH 2 A.EDWARDS,C.BOUNTRA JRNL TITL STRUCTURE OF THE HUMAN RAB38 IN COMPLEX WITH GTP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13318 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 697 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 958 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.2340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1398 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.63000 REMARK 3 B22 (A**2) : 2.96000 REMARK 3 B33 (A**2) : -1.33000 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): 0.166 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.014 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1554 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1454 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2105 ; 1.565 ; 1.649 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3380 ; 1.315 ; 1.581 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 195 ; 7.759 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 81 ;36.598 ;22.593 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 270 ;16.321 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;22.225 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 197 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1700 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 327 ; 0.001 ; 0.020 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): 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 : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6S5H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1292103140. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97624 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14044 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.10 REMARK 200 R MERGE FOR SHELL (I) : 0.64900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: 5OEC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % PEG3350, 10 % ETHYLENE GLYCOL, REMARK 280 0.1 M BIS-TRIS-PROPANE PH6 .5, 0.2 M SODIUM BROMIDE, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K 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 38.76150 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 38.76150 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 17.90200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.08700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.90200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.08700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.76150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.90200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.08700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.76150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.90200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.08700 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 C2 EDO A 308 LIES ON A SPECIAL POSITION. REMARK 375 BR BR A 313 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 505 LIES ON A SPECIAL POSITION. 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 132 REMARK 465 LYS A 133 REMARK 465 ASP A 134 REMARK 465 VAL A 135 REMARK 465 LEU A 136 REMARK 465 MET A 137 REMARK 465 ASN A 138 REMARK 465 CYS A 182 REMARK 465 ASP A 183 REMARK 465 LEU A 184 REMARK 465 MET A 185 REMARK 465 GLU A 186 REMARK 465 SER A 187 REMARK 465 ILE A 188 REMARK 465 GLU A 189 REMARK 465 PRO A 190 REMARK 465 ASP A 191 REMARK 465 VAL A 192 REMARK 465 VAL A 193 REMARK 465 LYS A 194 REMARK 465 PRO A 195 REMARK 465 HIS A 196 REMARK 465 LEU A 197 REMARK 465 THR A 198 REMARK 465 SER A 199 REMARK 465 THR A 200 REMARK 465 LYS A 201 REMARK 465 VAL A 202 REMARK 465 ALA A 203 REMARK 465 SER A 204 REMARK 465 CYS A 205 REMARK 465 SER A 206 REMARK 465 GLY A 207 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 SER A 0 OG REMARK 470 HIS A 5 CG ND1 CD2 CE1 NE2 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 OE2 GLU A 149 O2 EDO A 304 2.05 REMARK 500 OD1 ASN A 74 O HOH A 401 2.15 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 MET A 75 60.24 -119.93 REMARK 500 LYS A 128 30.81 74.31 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 311 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 23 OG1 REMARK 620 2 THR A 41 OG1 84.5 REMARK 620 3 GTP A 301 O2G 172.5 91.1 REMARK 620 4 GTP A 301 O2B 92.1 174.9 92.6 REMARK 620 5 HOH A 411 O 88.0 90.6 86.0 93.2 REMARK 620 6 HOH A 434 O 92.1 90.2 94.0 85.9 179.2 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 314 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: P57729 RELATED DB: TARGETTRACK DBREF 6S5H A 1 207 UNP P57729 RAB38_HUMAN 1 207 SEQADV 6S5H SER A 0 UNP P57729 EXPRESSION TAG SEQRES 1 A 208 SER MET GLN ALA PRO HIS LYS GLU HIS LEU TYR LYS LEU SEQRES 2 A 208 LEU VAL ILE GLY ASP LEU GLY VAL GLY LYS THR SER ILE SEQRES 3 A 208 ILE LYS ARG TYR VAL HIS GLN ASN PHE SER SER HIS TYR SEQRES 4 A 208 ARG ALA THR ILE GLY VAL ASP PHE ALA LEU LYS VAL LEU SEQRES 5 A 208 HIS TRP ASP PRO GLU THR VAL VAL ARG LEU GLN LEU TRP SEQRES 6 A 208 ASP ILE ALA GLY GLN GLU ARG PHE GLY ASN MET THR ARG SEQRES 7 A 208 VAL TYR TYR ARG GLU ALA MET GLY ALA PHE ILE VAL PHE SEQRES 8 A 208 ASP VAL THR ARG PRO ALA THR PHE GLU ALA VAL ALA LYS SEQRES 9 A 208 TRP LYS ASN ASP LEU ASP SER LYS LEU SER LEU PRO ASN SEQRES 10 A 208 GLY LYS PRO VAL SER VAL VAL LEU LEU ALA ASN LYS CYS SEQRES 11 A 208 ASP GLN GLY LYS ASP VAL LEU MET ASN ASN GLY LEU LYS SEQRES 12 A 208 MET ASP GLN PHE CYS LYS GLU HIS GLY PHE VAL GLY TRP SEQRES 13 A 208 PHE GLU THR SER ALA LYS GLU ASN ILE ASN ILE ASP GLU SEQRES 14 A 208 ALA SER ARG CYS LEU VAL LYS HIS ILE LEU ALA ASN GLU SEQRES 15 A 208 CYS ASP LEU MET GLU SER ILE GLU PRO ASP VAL VAL LYS SEQRES 16 A 208 PRO HIS LEU THR SER THR LYS VAL ALA SER CYS SER GLY HET GTP A 301 32 HET EDO A 302 4 HET EDO A 303 4 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET EDO A 308 4 HET EDO A 309 4 HET EDO A 310 4 HET MG A 311 1 HET BR A 312 1 HET BR A 313 1 HET BR A 314 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM BR BROMIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 EDO 9(C2 H6 O2) FORMUL 12 MG MG 2+ FORMUL 13 BR 3(BR 1-) FORMUL 16 HOH *145(H2 O) HELIX 1 AA1 GLY A 21 GLN A 32 1 12 HELIX 2 AA2 GLN A 69 GLY A 73 5 5 HELIX 3 AA3 MET A 75 ARG A 81 1 7 HELIX 4 AA4 ARG A 94 LEU A 112 1 19 HELIX 5 AA5 GLY A 140 GLY A 151 1 12 HELIX 6 AA6 ASN A 165 ASN A 180 1 16 SHEET 1 AA1 6 VAL A 44 ASP A 54 0 SHEET 2 AA1 6 THR A 57 ILE A 66 -1 O VAL A 59 N LEU A 51 SHEET 3 AA1 6 LYS A 6 ILE A 15 1 N HIS A 8 O ARG A 60 SHEET 4 AA1 6 ALA A 83 ASP A 91 1 O VAL A 89 N ILE A 15 SHEET 5 AA1 6 SER A 121 ASN A 127 1 O LEU A 125 N ILE A 88 SHEET 6 AA1 6 GLY A 154 THR A 158 1 O PHE A 156 N ALA A 126 LINK OG1 THR A 23 MG MG A 311 1555 1555 2.07 LINK OG1 THR A 41 MG MG A 311 1555 1555 2.11 LINK O2G GTP A 301 MG MG A 311 1555 1555 1.98 LINK O2B GTP A 301 MG MG A 311 1555 1555 2.08 LINK MG MG A 311 O HOH A 411 1555 1555 2.09 LINK MG MG A 311 O HOH A 434 1555 1555 2.14 SITE 1 AC1 26 LEU A 18 GLY A 19 VAL A 20 GLY A 21 SITE 2 AC1 26 LYS A 22 THR A 23 SER A 24 PHE A 34 SITE 3 AC1 26 SER A 35 SER A 36 TYR A 38 ALA A 40 SITE 4 AC1 26 THR A 41 GLY A 68 ASN A 127 LYS A 128 SITE 5 AC1 26 ASP A 130 SER A 159 ALA A 160 LYS A 161 SITE 6 AC1 26 EDO A 304 MG A 311 HOH A 411 HOH A 434 SITE 7 AC1 26 HOH A 454 HOH A 474 SITE 1 AC2 3 MET A 75 TYR A 79 HOH A 402 SITE 1 AC3 7 LYS A 27 ASN A 33 SER A 35 ARG A 39 SITE 2 AC3 7 ASP A 109 PRO A 119 HOH A 468 SITE 1 AC4 5 SER A 36 GLU A 149 LYS A 161 GTP A 301 SITE 2 AC4 5 HOH A 420 SITE 1 AC5 2 LEU A 18 HOH A 417 SITE 1 AC6 3 PHE A 46 ARG A 77 ARG A 81 SITE 1 AC7 5 VAL A 30 GLN A 32 LEU A 48 LYS A 49 SITE 2 AC7 5 VAL A 50 SITE 1 AC8 2 HOH A 418 HOH A 430 SITE 1 AC9 1 ASN A 139 SITE 1 AD1 4 PHE A 98 HOH A 410 HOH A 456 HOH A 471 SITE 1 AD2 5 THR A 23 THR A 41 GTP A 301 HOH A 411 SITE 2 AD2 5 HOH A 434 SITE 1 AD3 4 GLN A 69 ARG A 94 PRO A 95 ALA A 96 SITE 1 AD4 1 HOH A 506 SITE 1 AD5 3 ASN A 106 HIS A 150 HOH A 455 CRYST1 35.804 144.174 77.523 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 0.027930 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012899 0.00000