HEADER SIGNALING PROTEIN 10-SEP-19 6STG TITLE HUMAN RAB8A PHOSPHORYLATED AT SER111 IN COMPLEX WITH GPPNP 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 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PARKINSON DISEASE, PHOSPHORYLATION, SMALL G-PROTEIN, SF3 MOTIF, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VIEWEG,K.MULHOLLAND,B.BRAEUNING,N.KACHARIYA,Y.LAI,R.TOTH,M.SATTLER, AUTHOR 2 M.GROLL,A.ITZEN,M.M.K.MUQIT REVDAT 3 24-JAN-24 6STG 1 LINK REVDAT 2 20-MAY-20 6STG 1 JRNL REVDAT 1 22-APR-20 6STG 0 JRNL AUTH S.VIEWEG,K.MULHOLLAND,B.BRAUNING,N.KACHARIYA,Y.C.LAI,R.TOTH, JRNL AUTH 2 P.K.SINGH,I.VOLPI,M.SATTLER,M.GROLL,A.ITZEN,M.M.K.MUQIT JRNL TITL PINK1-DEPENDENT PHOSPHORYLATION OF SERINE111 WITHIN THE SF3 JRNL TITL 2 MOTIF OF RAB GTPASES IMPAIRS EFFECTOR INTERACTIONS AND JRNL TITL 3 LRRK2-MEDIATED PHOSPHORYLATION AT THREONINE72. JRNL REF BIOCHEM.J. V. 477 1651 2020 JRNL REFN ESSN 1470-8728 JRNL PMID 32227113 JRNL DOI 10.1042/BCJ20190664 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0253 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 11143 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 586 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 758 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.3690 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.4180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2762 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 9 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.20000 REMARK 3 B22 (A**2) : -2.88000 REMARK 3 B33 (A**2) : 5.43000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.35000 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): 0.371 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.351 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 37.080 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2876 ; 0.002 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2717 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3869 ; 1.184 ; 1.652 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6282 ; 1.055 ; 1.595 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 338 ; 5.515 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;31.421 ;22.025 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 547 ;17.906 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;19.538 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 388 ; 0.037 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3123 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 627 ; 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 : 2 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 902 REMARK 3 ORIGIN FOR THE GROUP (A): -21.0637 -2.4888 -47.1387 REMARK 3 T TENSOR REMARK 3 T11: 0.1501 T22: 0.1421 REMARK 3 T33: 0.0650 T12: -0.0085 REMARK 3 T13: -0.0927 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 1.3957 L22: 0.1621 REMARK 3 L33: 1.4616 L12: -0.1293 REMARK 3 L13: -0.0306 L23: 0.0589 REMARK 3 S TENSOR REMARK 3 S11: 0.0351 S12: 0.0502 S13: -0.0739 REMARK 3 S21: -0.0102 S22: -0.0467 S23: 0.0389 REMARK 3 S31: -0.0440 S32: -0.0150 S33: 0.0116 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 902 REMARK 3 ORIGIN FOR THE GROUP (A): -11.8933 -17.9199 -20.3822 REMARK 3 T TENSOR REMARK 3 T11: 0.1416 T22: 0.1889 REMARK 3 T33: 0.0577 T12: 0.0021 REMARK 3 T13: -0.0799 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.8984 L22: 1.2544 REMARK 3 L33: 0.8183 L12: -0.1174 REMARK 3 L13: 0.2991 L23: -0.7628 REMARK 3 S TENSOR REMARK 3 S11: 0.0123 S12: 0.0369 S13: 0.0770 REMARK 3 S21: 0.0550 S22: 0.0677 S23: -0.0247 REMARK 3 S31: 0.1244 S32: -0.0231 S33: -0.0800 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 : WITH TLS ADDED REMARK 4 REMARK 4 6STG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292104272. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11734 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.57800 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: PHASER REMARK 200 STARTING MODEL: 4LHW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 30% PEG300, PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 46.86000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 5 REMARK 465 HIS A 178 REMARK 465 HIS A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 MET B 5 REMARK 465 THR B 36 REMARK 465 PHE B 37 REMARK 465 HIS B 177 REMARK 465 HIS B 178 REMARK 465 HIS B 179 REMARK 465 HIS B 180 REMARK 465 HIS B 181 REMARK 465 HIS B 182 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 82 -53.11 69.36 REMARK 500 VAL B 125 75.01 -102.03 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 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 22 OG1 REMARK 620 2 THR A 40 OG1 70.6 REMARK 620 3 GNP A 901 O2G 108.9 65.5 REMARK 620 4 GNP A 901 O2B 74.1 122.5 85.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 22 OG1 REMARK 620 2 THR B 40 OG1 78.9 REMARK 620 3 GNP B 901 O1G 166.3 87.5 REMARK 620 4 GNP B 901 O2B 94.0 164.5 99.6 REMARK 620 N 1 2 3 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 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS B 903 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LHW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAB8 IN ITS ACTIVE GPPNHP-BOUND FORM DBREF 6STG A 6 176 UNP P61006 RAB8A_HUMAN 6 176 DBREF 6STG B 6 176 UNP P61006 RAB8A_HUMAN 6 176 SEQADV 6STG MET A 5 UNP P61006 INITIATING METHIONINE SEQADV 6STG HIS A 177 UNP P61006 EXPRESSION TAG SEQADV 6STG HIS A 178 UNP P61006 EXPRESSION TAG SEQADV 6STG HIS A 179 UNP P61006 EXPRESSION TAG SEQADV 6STG HIS A 180 UNP P61006 EXPRESSION TAG SEQADV 6STG HIS A 181 UNP P61006 EXPRESSION TAG SEQADV 6STG HIS A 182 UNP P61006 EXPRESSION TAG SEQADV 6STG MET B 5 UNP P61006 INITIATING METHIONINE SEQADV 6STG HIS B 177 UNP P61006 EXPRESSION TAG SEQADV 6STG HIS B 178 UNP P61006 EXPRESSION TAG SEQADV 6STG HIS B 179 UNP P61006 EXPRESSION TAG SEQADV 6STG HIS B 180 UNP P61006 EXPRESSION TAG SEQADV 6STG HIS B 181 UNP P61006 EXPRESSION TAG SEQADV 6STG HIS B 182 UNP P61006 EXPRESSION TAG SEQRES 1 A 178 MET ASP TYR LEU PHE LYS LEU LEU LEU ILE GLY ASP SER SEQRES 2 A 178 GLY VAL GLY LYS THR CYS VAL LEU PHE ARG PHE SER GLU SEQRES 3 A 178 ASP ALA PHE ASN SER THR PHE ILE SER THR ILE GLY ILE SEQRES 4 A 178 ASP PHE LYS ILE ARG THR ILE GLU LEU ASP GLY LYS ARG SEQRES 5 A 178 ILE LYS LEU GLN ILE TRP ASP THR ALA GLY GLN GLU ARG SEQRES 6 A 178 PHE ARG THR ILE THR THR ALA TYR TYR ARG GLY ALA MET SEQRES 7 A 178 GLY ILE MET LEU VAL TYR ASP ILE THR ASN GLU LYS SER SEQRES 8 A 178 PHE ASP ASN ILE ARG ASN TRP ILE ARG ASN ILE GLU GLU SEQRES 9 A 178 HIS ALA SEP ALA ASP VAL GLU LYS MET ILE LEU GLY ASN SEQRES 10 A 178 LYS CYS ASP VAL ASN ASP LYS ARG GLN VAL SER LYS GLU SEQRES 11 A 178 ARG GLY GLU LYS LEU ALA LEU ASP TYR GLY ILE LYS PHE SEQRES 12 A 178 MET GLU THR SER ALA LYS ALA ASN ILE ASN VAL GLU ASN SEQRES 13 A 178 ALA PHE PHE THR LEU ALA ARG ASP ILE LYS ALA LYS MET SEQRES 14 A 178 ASP LYS LYS HIS HIS HIS HIS HIS HIS SEQRES 1 B 178 MET ASP TYR LEU PHE LYS LEU LEU LEU ILE GLY ASP SER SEQRES 2 B 178 GLY VAL GLY LYS THR CYS VAL LEU PHE ARG PHE SER GLU SEQRES 3 B 178 ASP ALA PHE ASN SER THR PHE ILE SER THR ILE GLY ILE SEQRES 4 B 178 ASP PHE LYS ILE ARG THR ILE GLU LEU ASP GLY LYS ARG SEQRES 5 B 178 ILE LYS LEU GLN ILE TRP ASP THR ALA GLY GLN GLU ARG SEQRES 6 B 178 PHE ARG THR ILE THR THR ALA TYR TYR ARG GLY ALA MET SEQRES 7 B 178 GLY ILE MET LEU VAL TYR ASP ILE THR ASN GLU LYS SER SEQRES 8 B 178 PHE ASP ASN ILE ARG ASN TRP ILE ARG ASN ILE GLU GLU SEQRES 9 B 178 HIS ALA SEP ALA ASP VAL GLU LYS MET ILE LEU GLY ASN SEQRES 10 B 178 LYS CYS ASP VAL ASN ASP LYS ARG GLN VAL SER LYS GLU SEQRES 11 B 178 ARG GLY GLU LYS LEU ALA LEU ASP TYR GLY ILE LYS PHE SEQRES 12 B 178 MET GLU THR SER ALA LYS ALA ASN ILE ASN VAL GLU ASN SEQRES 13 B 178 ALA PHE PHE THR LEU ALA ARG ASP ILE LYS ALA LYS MET SEQRES 14 B 178 ASP LYS LYS HIS HIS HIS HIS HIS HIS MODRES 6STG SEP A 111 SER MODIFIED RESIDUE MODRES 6STG SEP B 111 SER MODIFIED RESIDUE HET SEP A 111 10 HET SEP B 111 10 HET GNP A 901 32 HET MG A 902 1 HET GNP B 901 32 HET MG B 902 1 HET TRS B 903 8 HETNAM SEP PHOSPHOSERINE HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN SEP PHOSPHONOSERINE HETSYN TRS TRIS BUFFER FORMUL 1 SEP 2(C3 H8 N O6 P) FORMUL 3 GNP 2(C10 H17 N6 O13 P3) FORMUL 4 MG 2(MG 2+) FORMUL 7 TRS C4 H12 N O3 1+ FORMUL 8 HOH *9(H2 O) HELIX 1 AA1 GLY A 20 ASP A 31 1 12 HELIX 2 AA2 GLN A 67 ARG A 69 5 3 HELIX 3 AA3 PHE A 70 ALA A 76 1 7 HELIX 4 AA4 TYR A 77 ARG A 79 5 3 HELIX 5 AA5 ASN A 92 ALA A 110 1 19 HELIX 6 AA6 SER A 132 GLY A 144 1 13 HELIX 7 AA7 ASN A 157 LYS A 175 1 19 HELIX 8 AA8 GLY B 20 GLU B 30 1 11 HELIX 9 AA9 GLN B 67 ARG B 69 5 3 HELIX 10 AB1 PHE B 70 ALA B 76 1 7 HELIX 11 AB2 ASN B 92 ALA B 110 1 19 HELIX 12 AB3 VAL B 125 ARG B 129 5 5 HELIX 13 AB4 SER B 132 GLY B 144 1 13 HELIX 14 AB5 ASN B 157 LYS B 176 1 20 SHEET 1 AA1 6 ASP A 44 LEU A 52 0 SHEET 2 AA1 6 LYS A 55 ASP A 63 -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 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 ASP B 44 LEU B 52 0 SHEET 2 AA2 6 LYS B 55 ASP B 63 -1 O ILE B 57 N ILE B 50 SHEET 3 AA2 6 TYR B 7 ILE B 14 1 N TYR B 7 O LYS B 58 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 C ALA A 110 N SEP A 111 1555 1555 1.34 LINK C SEP A 111 N ALA A 112 1555 1555 1.34 LINK C ALA B 110 N SEP B 111 1555 1555 1.34 LINK C SEP B 111 N ALA B 112 1555 1555 1.34 LINK OG1 THR A 22 MG MG A 902 1555 1555 2.31 LINK OG1 THR A 40 MG MG A 902 1555 1555 2.39 LINK O2G GNP A 901 MG MG A 902 1555 1555 2.46 LINK O2B GNP A 901 MG MG A 902 1555 1555 2.34 LINK OG1 THR B 22 MG MG B 902 1555 1555 2.12 LINK OG1 THR B 40 MG MG B 902 1555 1555 2.30 LINK O1G GNP B 901 MG MG B 902 1555 1555 2.25 LINK O2B GNP B 901 MG MG B 902 1555 1555 2.05 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 VAL A 125 SER A 151 ALA A 152 SITE 6 AC1 23 LYS A 153 MG A 902 HOH A1001 SITE 1 AC2 5 THR A 22 THR A 40 ASP A 63 THR A 64 SITE 2 AC2 5 GNP A 901 SITE 1 AC3 22 ASP B 16 SER B 17 GLY B 18 VAL B 19 SITE 2 AC3 22 GLY B 20 LYS B 21 THR B 22 CYS B 23 SITE 3 AC3 22 PHE B 33 SER B 35 ILE B 38 SER B 39 SITE 4 AC3 22 THR B 40 GLY B 66 ASN B 121 LYS B 122 SITE 5 AC3 22 ASP B 124 VAL B 125 SER B 151 ALA B 152 SITE 6 AC3 22 LYS B 153 MG B 902 SITE 1 AC4 4 THR B 22 ILE B 38 THR B 40 GNP B 901 SITE 1 AC5 6 HIS A 109 ALA A 110 SEP A 111 GLU B 108 SITE 2 AC5 6 HIS B 109 SEP B 111 CRYST1 34.920 93.720 56.120 90.00 102.97 90.00 P 1 21 1 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 0.028637 0.000000 0.006597 0.00000 SCALE2 0.000000 0.010670 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018286 0.00000