PDB Short entry for 6WCW HEADER METAL BINDING PROTEIN 31-MAR-20 6WCW TITLE STRUCTURE OF HUMAN RUBICON RH DOMAIN IN COMPLEX WITH GTP-BOUND RAB7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-7A; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RUN DOMAIN BECLIN-1-INTERACTING AND CYSTEINE-RICH DOMAIN- COMPND 8 CONTAINING PROTEIN; COMPND 9 CHAIN: A; COMPND 10 FRAGMENT: RH DOMAIN; COMPND 11 SYNONYM: RUBICON, BECLIN-1 ASSOCIATED RUN DOMAIN CONTAINING PROTEIN, COMPND 12 BARON; COMPND 13 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: RAB7A, RAB7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RUBCN, KIAA0226; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS AUTOPHAGY, RAB, GTPASE, AGING, ZINC FINGER, G PROTEIN, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.K.BHARGAVA,J.M.BYCK,D.P.FARRELL,I.ANISHCHENKO,F.DIMAIO,Y.J.IM, AUTHOR 2 J.H.HURLEY REVDAT 4 18-OCT-23 6WCW 1 REMARK REVDAT 3 05-AUG-20 6WCW 1 JRNL LINK REVDAT 2 22-JUL-20 6WCW 1 JRNL REVDAT 1 01-JUL-20 6WCW 0 JRNL AUTH H.K.BHARGAVA,K.TABATA,J.M.BYCK,M.HAMASAKI,D.P.FARRELL, JRNL AUTH 2 I.ANISHCHENKO,F.DIMAIO,Y.J.IM,T.YOSHIMORI,J.H.HURLEY JRNL TITL STRUCTURAL BASIS FOR AUTOPHAGY INHIBITION BY THE HUMAN JRNL TITL 2 RUBICON-RAB7 COMPLEX. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 17003 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32632011 JRNL DOI 10.1073/PNAS.2008030117 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 12395 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 591 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 54.2200 - 4.4400 0.99 3025 155 0.1735 0.2353 REMARK 3 2 4.4400 - 3.5300 0.99 2958 137 0.1749 0.2124 REMARK 3 3 3.5300 - 3.0800 0.99 2898 169 0.2443 0.3102 REMARK 3 4 3.0800 - 2.8000 0.99 2923 130 0.2824 0.3922 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.384 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.199 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.14 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 : 0.009 3512 REMARK 3 ANGLE : 1.054 4748 REMARK 3 CHIRALITY : 0.056 521 REMARK 3 PLANARITY : 0.006 607 REMARK 3 DIHEDRAL : 24.585 1320 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): -3.9739 24.7072 38.6235 REMARK 3 T TENSOR REMARK 3 T11: 0.2649 T22: 0.3755 REMARK 3 T33: 0.3226 T12: 0.0320 REMARK 3 T13: -0.0048 T23: 0.0958 REMARK 3 L TENSOR REMARK 3 L11: 0.2089 L22: -0.0073 REMARK 3 L33: 2.4046 L12: 0.2259 REMARK 3 L13: -1.0671 L23: -0.3805 REMARK 3 S TENSOR REMARK 3 S11: 0.0467 S12: 0.0857 S13: 0.0241 REMARK 3 S21: 0.0111 S22: 0.0599 S23: 0.0001 REMARK 3 S31: -0.0456 S32: -0.3069 S33: -0.0391 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 6WCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000247762. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.283 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12498 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 92.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: 1YHN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% (W/V) PEG 8000, 100MM TRIS-HCL PH REMARK 280 7.4, 15MM TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 16.24200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.66500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 92.11377 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 16.24200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.66500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 92.11377 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 SER B -1 REMARK 465 ASN B 0 REMARK 465 ALA B 1 REMARK 465 THR B 2 REMARK 465 SER B 3 REMARK 465 ARG B 4 REMARK 465 LYS B 5 REMARK 465 LYS B 6 REMARK 465 SER A 696 REMARK 465 ARG A 944 REMARK 465 GLN A 945 REMARK 465 SER A 946 REMARK 465 LEU A 947 REMARK 465 GLU A 948 REMARK 465 SER A 949 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 LEU A 906 NZ LYS A 921 2.05 REMARK 500 NH2 ARG B 132 OE2 GLU B 153 2.09 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 NH2 ARG B 113 O HIS A 705 4455 2.05 REMARK 500 O LYS A 860 NZ LYS A 925 4455 2.16 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 CYS A 923 CA - CB - SG ANGL. DEV. = 7.3 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 ASP B 54 -16.48 69.14 REMARK 500 LEU B 67 -99.99 -65.18 REMARK 500 GLU B 68 44.34 -160.78 REMARK 500 ARG B 69 42.63 -98.66 REMARK 500 SER B 72 -17.18 70.36 REMARK 500 VAL B 75 25.12 -149.38 REMARK 500 ASP B 114 71.64 58.26 REMARK 500 LYS B 126 34.66 81.06 REMARK 500 ASN B 148 61.49 63.68 REMARK 500 ILE A 701 -38.20 -131.92 REMARK 500 GLN A 717 40.91 -107.57 REMARK 500 TRP A 766 53.61 -91.13 REMARK 500 ALA A 829 50.08 -102.90 REMARK 500 LYS A 916 7.46 58.47 REMARK 500 PHE A 924 -91.00 -96.79 REMARK 500 LYS A 925 -45.03 5.23 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 B1402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 22 OG1 REMARK 620 2 THR B 40 OG1 136.2 REMARK 620 3 GTP B1401 O1G 120.6 86.6 REMARK 620 4 GTP B1401 O2B 71.6 152.1 73.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 721 SG REMARK 620 2 CYS A 724 SG 106.5 REMARK 620 3 CYS A 747 SG 122.1 119.5 REMARK 620 4 CYS A 750 SG 108.6 99.5 97.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 826 SG REMARK 620 2 HIS A 877 NE2 136.1 REMARK 620 3 CYS A 881 SG 105.4 95.3 REMARK 620 4 CYS A 884 SG 100.3 107.0 112.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 891 SG REMARK 620 2 CYS A 894 SG 103.2 REMARK 620 3 HIS A 920 ND1 117.6 105.9 REMARK 620 4 CYS A 923 SG 102.2 111.1 116.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1004 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 912 SG REMARK 620 2 CYS A 915 SG 93.5 REMARK 620 3 CYS A 929 SG 114.0 84.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP B 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1004 DBREF 6WCW B 2 182 UNP P51149 RAB7A_HUMAN 2 182 DBREF 6WCW A 699 949 UNP Q92622 RUBIC_HUMAN 699 949 SEQADV 6WCW SER B -1 UNP P51149 EXPRESSION TAG SEQADV 6WCW ASN B 0 UNP P51149 EXPRESSION TAG SEQADV 6WCW ALA B 1 UNP P51149 EXPRESSION TAG SEQADV 6WCW LEU B 67 UNP P51149 GLN 67 ENGINEERED MUTATION SEQADV 6WCW SER A 696 UNP Q92622 EXPRESSION TAG SEQADV 6WCW ASN A 697 UNP Q92622 EXPRESSION TAG SEQADV 6WCW ALA A 698 UNP Q92622 EXPRESSION TAG SEQRES 1 B 184 SER ASN ALA THR SER ARG LYS LYS VAL LEU LEU LYS VAL SEQRES 2 B 184 ILE ILE LEU GLY ASP SER GLY VAL GLY LYS THR SER LEU SEQRES 3 B 184 MET ASN GLN TYR VAL ASN LYS LYS PHE SER ASN GLN TYR SEQRES 4 B 184 LYS ALA THR ILE GLY ALA ASP PHE LEU THR LYS GLU VAL SEQRES 5 B 184 MET VAL ASP ASP ARG LEU VAL THR MET GLN ILE TRP ASP SEQRES 6 B 184 THR ALA GLY LEU GLU ARG PHE GLN SER LEU GLY VAL ALA SEQRES 7 B 184 PHE TYR ARG GLY ALA ASP CYS CYS VAL LEU VAL PHE ASP SEQRES 8 B 184 VAL THR ALA PRO ASN THR PHE LYS THR LEU ASP SER TRP SEQRES 9 B 184 ARG ASP GLU PHE LEU ILE GLN ALA SER PRO ARG ASP PRO SEQRES 10 B 184 GLU ASN PHE PRO PHE VAL VAL LEU GLY ASN LYS ILE ASP SEQRES 11 B 184 LEU GLU ASN ARG GLN VAL ALA THR LYS ARG ALA GLN ALA SEQRES 12 B 184 TRP CYS TYR SER LYS ASN ASN ILE PRO TYR PHE GLU THR SEQRES 13 B 184 SER ALA LYS GLU ALA ILE ASN VAL GLU GLN ALA PHE GLN SEQRES 14 B 184 THR ILE ALA ARG ASN ALA LEU LYS GLN GLU THR GLU VAL SEQRES 15 B 184 GLU LEU SEQRES 1 A 254 SER ASN ALA GLN ILE ILE PHE ASN VAL HIS PRO ALA PRO SEQRES 2 A 254 THR ARG LYS ILE ALA VAL ALA LYS GLN ASN TYR ARG CYS SEQRES 3 A 254 ALA GLY CYS GLY ILE ARG THR ASP PRO ASP TYR ILE LYS SEQRES 4 A 254 ARG LEU ARG TYR CYS GLU TYR LEU GLY LYS TYR PHE CYS SEQRES 5 A 254 GLN CYS CYS HIS GLU ASN ALA GLN MET ALA ILE PRO SER SEQRES 6 A 254 ARG VAL LEU ARG LYS TRP ASP PHE SER LYS TYR TYR VAL SEQRES 7 A 254 SER ASN PHE SER LYS ASP LEU LEU ILE LYS ILE TRP ASN SEQRES 8 A 254 ASP PRO LEU PHE ASN VAL GLN ASP ILE ASN SER ALA LEU SEQRES 9 A 254 TYR ARG LYS VAL LYS LEU LEU ASN GLN VAL ARG LEU LEU SEQRES 10 A 254 ARG VAL GLN LEU CYS HIS MET LYS ASN MET PHE LYS THR SEQRES 11 A 254 CYS ARG LEU ALA LYS GLU LEU LEU ASP SER PHE ASP THR SEQRES 12 A 254 VAL PRO GLY HIS LEU THR GLU ASP LEU HIS LEU TYR SER SEQRES 13 A 254 LEU ASN ASP LEU THR ALA THR ARG LYS GLY GLU LEU GLY SEQRES 14 A 254 PRO ARG LEU ALA GLU LEU THR ARG ALA GLY ALA THR HIS SEQRES 15 A 254 VAL GLU ARG CYS MET LEU CYS GLN ALA LYS GLY PHE ILE SEQRES 16 A 254 CYS GLU PHE CYS GLN ASN GLU ASP ASP ILE ILE PHE PRO SEQRES 17 A 254 PHE GLU LEU HIS LYS CYS ARG THR CYS GLU GLU CYS LYS SEQRES 18 A 254 ALA CYS TYR HIS LYS ALA CYS PHE LYS SER GLY SER CYS SEQRES 19 A 254 PRO ARG CYS GLU ARG LEU GLN ALA ARG ARG GLU ALA LEU SEQRES 20 A 254 ALA ARG GLN SER LEU GLU SER HET GTP B1401 32 HET MG B1402 1 HET ZN A1001 1 HET ZN A1002 1 HET ZN A1003 1 HET ZN A1004 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION FORMUL 3 GTP C10 H16 N5 O14 P3 FORMUL 4 MG MG 2+ FORMUL 5 ZN 4(ZN 2+) HELIX 1 AA1 GLY B 20 LYS B 31 1 12 HELIX 2 AA2 VAL B 75 ARG B 79 5 5 HELIX 3 AA3 ALA B 92 THR B 98 1 7 HELIX 4 AA4 THR B 98 SER B 111 1 14 HELIX 5 AA5 ASP B 114 PHE B 118 5 5 HELIX 6 AA6 ALA B 135 LYS B 146 1 12 HELIX 7 AA7 ASN B 161 THR B 178 1 18 HELIX 8 AA8 ALA A 707 GLN A 717 1 11 HELIX 9 AA9 ASP A 729 LEU A 736 5 8 HELIX 10 AB1 ILE A 758 ARG A 764 1 7 HELIX 11 AB2 SER A 774 ILE A 784 1 11 HELIX 12 AB3 VAL A 792 ASN A 796 1 5 HELIX 13 AB4 ALA A 798 VAL A 803 1 6 HELIX 14 AB5 VAL A 803 LYS A 824 1 22 HELIX 15 AB6 ALA A 829 PHE A 836 1 8 HELIX 16 AB7 PRO A 840 ASP A 846 1 7 HELIX 17 AB8 SER A 851 LYS A 860 1 10 HELIX 18 AB9 GLU A 862 CYS A 881 1 20 HELIX 19 AC1 CYS A 884 GLY A 888 5 5 HELIX 20 AC2 CYS A 929 ALA A 943 1 15 SHEET 1 AA1 6 ASP B 44 VAL B 52 0 SHEET 2 AA1 6 ARG B 55 ASP B 63 -1 O MET B 59 N LYS B 48 SHEET 3 AA1 6 LEU B 8 LEU B 14 1 N ILE B 13 O TRP B 62 SHEET 4 AA1 6 CYS B 83 ASP B 89 1 O VAL B 85 N LEU B 14 SHEET 5 AA1 6 PHE B 120 ASN B 125 1 O ASN B 125 N PHE B 88 SHEET 6 AA1 6 TYR B 151 THR B 154 1 O PHE B 152 N GLY B 124 SHEET 1 AA2 2 ARG A 737 TYR A 738 0 SHEET 2 AA2 2 TYR A 745 PHE A 746 -1 O PHE A 746 N ARG A 737 SHEET 1 AA3 2 ALA A 754 MET A 756 0 SHEET 2 AA3 2 TYR A 771 VAL A 773 -1 O VAL A 773 N ALA A 754 SHEET 1 AA4 2 PHE A 790 ASN A 791 0 SHEET 2 AA4 2 LEU A 849 TYR A 850 -1 O TYR A 850 N PHE A 790 SHEET 1 AA5 2 CYS A 909 THR A 911 0 SHEET 2 AA5 2 CYS A 918 HIS A 920 -1 O TYR A 919 N ARG A 910 LINK OG1 THR B 22 MG MG B1402 1555 1555 1.84 LINK OG1 THR B 40 MG MG B1402 1555 1555 2.02 LINK O1G GTP B1401 MG MG B1402 1555 1555 1.86 LINK O2B GTP B1401 MG MG B1402 1555 1555 2.26 LINK SG CYS A 721 ZN ZN A1001 1555 1555 1.98 LINK SG CYS A 724 ZN ZN A1001 1555 1555 2.04 LINK SG CYS A 747 ZN ZN A1001 1555 1555 2.01 LINK SG CYS A 750 ZN ZN A1001 1555 1555 2.23 LINK SG CYS A 826 ZN ZN A1002 1555 1555 2.12 LINK NE2 HIS A 877 ZN ZN A1002 1555 1555 1.83 LINK SG CYS A 881 ZN ZN A1002 1555 1555 2.28 LINK SG CYS A 884 ZN ZN A1002 1555 1555 2.15 LINK SG CYS A 891 ZN ZN A1003 1555 1555 2.11 LINK SG CYS A 894 ZN ZN A1003 1555 1555 2.23 LINK SG CYS A 912 ZN ZN A1004 1555 1555 2.34 LINK SG CYS A 915 ZN ZN A1004 1555 1555 2.34 LINK ND1 HIS A 920 ZN ZN A1003 1555 1555 1.85 LINK SG CYS A 923 ZN ZN A1003 1555 1555 2.03 LINK SG CYS A 929 ZN ZN A1004 1555 1555 2.44 SITE 1 AC1 22 SER B 17 GLY B 18 VAL B 19 GLY B 20 SITE 2 AC1 22 LYS B 21 THR B 22 SER B 23 PHE B 33 SITE 3 AC1 22 SER B 34 ASN B 35 TYR B 37 THR B 40 SITE 4 AC1 22 THR B 64 GLY B 66 ASN B 125 LYS B 126 SITE 5 AC1 22 ASP B 128 LEU B 129 SER B 155 ALA B 156 SITE 6 AC1 22 LYS B 157 MG B1402 SITE 1 AC2 6 LYS B 21 THR B 22 THR B 40 ASP B 63 SITE 2 AC2 6 THR B 64 GTP B1401 SITE 1 AC3 4 CYS A 721 CYS A 724 CYS A 747 CYS A 750 SITE 1 AC4 4 CYS A 826 HIS A 877 CYS A 881 CYS A 884 SITE 1 AC5 4 CYS A 891 CYS A 894 HIS A 920 CYS A 923 SITE 1 AC6 4 CYS A 912 CYS A 915 CYS A 929 CYS A 932 CRYST1 60.040 45.330 186.277 90.00 98.51 90.00 I 1 2 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 0.016656 0.000000 0.002491 0.00000 SCALE2 0.000000 0.022060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005428 0.00000