PDB Short entry for 3NKV HEADER PROTEIN TRANSPORT 21-JUN-10 3NKV TITLE CRYSTAL STRUCTURE OF RAB1B COVALENTLY MODIFIED WITH AMP AT Y77 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-1B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RAB1B-AMP; 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: RAB1B, RAB1B_HUMAN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMAL KEYWDS POSTTRANSLATIONAL MODIFICATION, AMPYLATION, ADENYLYLATION, RAB1B, KEYWDS 2 VESICULAR TRANSPORT, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.P.MUELLER,H.PETERS,W.BLANKENFELDT,R.S.GOODY,A.ITZEN REVDAT 3 23-AUG-17 3NKV 1 REMARK REVDAT 2 22-SEP-10 3NKV 1 JRNL REVDAT 1 04-AUG-10 3NKV 0 JRNL AUTH M.P.MULLER,H.PETERS,J.BLUMER,W.BLANKENFELDT,R.S.GOODY, JRNL AUTH 2 A.ITZEN JRNL TITL THE LEGIONELLA EFFECTOR PROTEIN DRRA AMPYLATES THE MEMBRANE JRNL TITL 2 TRAFFIC REGULATOR RAB1B. JRNL REF SCIENCE V. 329 946 2010 JRNL REFN ISSN 0036-8075 JRNL PMID 20651120 JRNL DOI 10.1126/SCIENCE.1192276 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 31709 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) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1658 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2366 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 129 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2701 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 112 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : -1.40000 REMARK 3 B33 (A**2) : 0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.45000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.830 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2891 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1914 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3930 ; 2.053 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4674 ; 1.060 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 346 ; 6.064 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;36.981 ;24.488 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 517 ;14.405 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;15.547 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 451 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3115 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 595 ; 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): 1685 ; 1.395 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 697 ; 0.475 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2723 ; 2.421 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1204 ; 3.620 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1197 ; 5.726 ; 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 : 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 -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -3.2630 21.8830 -2.4050 REMARK 3 T TENSOR REMARK 3 T11: 0.0244 T22: 0.0458 REMARK 3 T33: 0.0390 T12: 0.0050 REMARK 3 T13: 0.0137 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 1.5080 L22: 1.0420 REMARK 3 L33: 1.7764 L12: 0.4846 REMARK 3 L13: 0.1943 L23: 0.4799 REMARK 3 S TENSOR REMARK 3 S11: -0.1245 S12: 0.0693 S13: -0.0242 REMARK 3 S21: 0.0232 S22: 0.1130 S23: -0.0052 REMARK 3 S31: 0.0805 S32: -0.0319 S33: 0.0115 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 -10 B 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -4.5870 -6.1690 -19.7160 REMARK 3 T TENSOR REMARK 3 T11: 0.0439 T22: 0.0275 REMARK 3 T33: 0.0490 T12: -0.0105 REMARK 3 T13: 0.0084 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 1.0081 L22: 0.8355 REMARK 3 L33: 1.1973 L12: -0.3233 REMARK 3 L13: 0.0889 L23: -0.1415 REMARK 3 S TENSOR REMARK 3 S11: 0.1129 S12: 0.0017 S13: -0.1193 REMARK 3 S21: -0.1330 S22: -0.0253 S23: 0.0239 REMARK 3 S31: -0.0245 S32: 0.0228 S33: -0.0876 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: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3NKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059956. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33392 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% (V/V) ISOPROPANOL, 15% (W/V) REMARK 280 PEG4000, 0.1 M IMIDAZOLE, 10 MM BACL2, PH 6.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 50.29450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 0 REMARK 465 HIS A 1 REMARK 465 MET A 2 REMARK 465 PRO A 3 REMARK 465 GLY A 174 REMARK 465 GLY B 0 REMARK 465 HIS B 1 REMARK 465 MET B 2 REMARK 465 PRO B 3 REMARK 465 GLU B 112 REMARK 465 GLY B 174 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 HOH B 180 O HOH B 226 2.05 REMARK 500 OH TYR B 77 O5' AMP B 600 2.11 REMARK 500 O HOH B 179 O HOH B 198 2.13 REMARK 500 CD GLN B 160 O HOH B 237 2.17 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 ASP A 16 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 MET A 165 CG - SD - CE ANGL. DEV. = -24.1 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 ALA B 110 -124.29 -112.15 REMARK 500 LYS B 122 33.57 78.21 REMARK 500 ALA B 155 -2.82 78.38 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 500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GNP A 400 O2G REMARK 620 2 GNP A 400 O2B 95.7 REMARK 620 3 HOH A 218 O 92.5 88.9 REMARK 620 4 HOH A 189 O 92.7 89.6 174.7 REMARK 620 5 SER A 22 OG 172.3 91.8 85.9 89.1 REMARK 620 6 THR A 40 OG1 89.8 173.7 88.0 93.0 82.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 22 OG REMARK 620 2 GNP B 400 O2G 174.1 REMARK 620 3 HOH B 185 O 91.4 92.1 REMARK 620 4 HOH B 199 O 88.2 88.7 175.3 REMARK 620 5 THR B 40 OG1 82.5 92.4 93.2 91.3 REMARK 620 6 GNP B 400 O2B 89.7 95.4 86.5 88.9 172.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 175 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 187 O REMARK 620 2 HOH B 301 O 119.4 REMARK 620 3 THR B 134 OG1 66.5 78.6 REMARK 620 4 ASP B 132 OD2 126.5 77.3 68.7 REMARK 620 5 HOH B 228 O 67.4 153.4 81.8 78.9 REMARK 620 6 ASP B 132 OD1 162.0 76.5 112.2 44.7 94.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA A 175 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 261 O REMARK 620 2 VAL A 43 O 70.9 REMARK 620 3 ASP A 44 OD1 130.1 63.8 REMARK 620 4 ILE A 41 O 81.4 98.8 85.9 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 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA A 175 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 175 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP B 600 DBREF 3NKV A 3 174 UNP Q9H0U4 RAB1B_HUMAN 3 174 DBREF 3NKV B 3 174 UNP Q9H0U4 RAB1B_HUMAN 3 174 SEQADV 3NKV GLY A 0 UNP Q9H0U4 EXPRESSION TAG SEQADV 3NKV HIS A 1 UNP Q9H0U4 EXPRESSION TAG SEQADV 3NKV MET A 2 UNP Q9H0U4 EXPRESSION TAG SEQADV 3NKV GLY B 0 UNP Q9H0U4 EXPRESSION TAG SEQADV 3NKV HIS B 1 UNP Q9H0U4 EXPRESSION TAG SEQADV 3NKV MET B 2 UNP Q9H0U4 EXPRESSION TAG SEQRES 1 A 175 GLY HIS MET PRO GLU TYR ASP TYR LEU PHE LYS LEU LEU SEQRES 2 A 175 LEU ILE GLY ASP SER GLY VAL GLY LYS SER CYS LEU LEU SEQRES 3 A 175 LEU ARG PHE ALA ASP ASP THR TYR THR GLU SER TYR ILE SEQRES 4 A 175 SER THR ILE GLY VAL ASP PHE LYS ILE ARG THR ILE GLU SEQRES 5 A 175 LEU ASP GLY LYS THR ILE LYS LEU GLN ILE TRP ASP THR SEQRES 6 A 175 ALA GLY GLN GLU ARG PHE ARG THR ILE THR SER SER TYR SEQRES 7 A 175 TYR ARG GLY ALA HIS GLY ILE ILE VAL VAL TYR ASP VAL SEQRES 8 A 175 THR ASP GLN GLU SER TYR ALA ASN VAL LYS GLN TRP LEU SEQRES 9 A 175 GLN GLU ILE ASP ARG TYR ALA SER GLU ASN VAL ASN LYS SEQRES 10 A 175 LEU LEU VAL GLY ASN LYS SER ASP LEU THR THR LYS LYS SEQRES 11 A 175 VAL VAL ASP ASN THR THR ALA LYS GLU PHE ALA ASP SER SEQRES 12 A 175 LEU GLY ILE PRO PHE LEU GLU THR SER ALA LYS ASN ALA SEQRES 13 A 175 THR ASN VAL GLU GLN ALA PHE MET THR MET ALA ALA GLU SEQRES 14 A 175 ILE LYS LYS ARG MET GLY SEQRES 1 B 175 GLY HIS MET PRO GLU TYR ASP TYR LEU PHE LYS LEU LEU SEQRES 2 B 175 LEU ILE GLY ASP SER GLY VAL GLY LYS SER CYS LEU LEU SEQRES 3 B 175 LEU ARG PHE ALA ASP ASP THR TYR THR GLU SER TYR ILE SEQRES 4 B 175 SER THR ILE GLY VAL ASP PHE LYS ILE ARG THR ILE GLU SEQRES 5 B 175 LEU ASP GLY LYS THR ILE LYS LEU GLN ILE TRP ASP THR SEQRES 6 B 175 ALA GLY GLN GLU ARG PHE ARG THR ILE THR SER SER TYR SEQRES 7 B 175 TYR ARG GLY ALA HIS GLY ILE ILE VAL VAL TYR ASP VAL SEQRES 8 B 175 THR ASP GLN GLU SER TYR ALA ASN VAL LYS GLN TRP LEU SEQRES 9 B 175 GLN GLU ILE ASP ARG TYR ALA SER GLU ASN VAL ASN LYS SEQRES 10 B 175 LEU LEU VAL GLY ASN LYS SER ASP LEU THR THR LYS LYS SEQRES 11 B 175 VAL VAL ASP ASN THR THR ALA LYS GLU PHE ALA ASP SER SEQRES 12 B 175 LEU GLY ILE PRO PHE LEU GLU THR SER ALA LYS ASN ALA SEQRES 13 B 175 THR ASN VAL GLU GLN ALA PHE MET THR MET ALA ALA GLU SEQRES 14 B 175 ILE LYS LYS ARG MET GLY HET GNP A 400 32 HET MG A 500 1 HET BA A 175 1 HET AMP A 600 22 HET GNP B 400 32 HET MG B 500 1 HET BA B 175 1 HET AMP B 600 22 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM BA BARIUM ION HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 3 GNP 2(C10 H17 N6 O13 P3) FORMUL 4 MG 2(MG 2+) FORMUL 5 BA 2(BA 2+) FORMUL 6 AMP 2(C10 H14 N5 O7 P) FORMUL 11 HOH *245(H2 O) HELIX 1 1 GLY A 20 ASP A 31 1 12 HELIX 2 2 GLN A 67 ARG A 69 5 3 HELIX 3 3 PHE A 70 SER A 76 1 7 HELIX 4 4 ASP A 92 ASN A 98 1 7 HELIX 5 5 ASN A 98 ALA A 110 1 13 HELIX 6 6 ASP A 132 LEU A 143 1 12 HELIX 7 7 ASN A 157 ARG A 172 1 16 HELIX 8 8 GLY B 20 ASP B 31 1 12 HELIX 9 9 GLN B 67 ARG B 69 5 3 HELIX 10 10 PHE B 70 SER B 76 1 7 HELIX 11 11 ASP B 92 ASN B 98 1 7 HELIX 12 12 ASN B 98 ALA B 110 1 13 HELIX 13 13 LEU B 125 LYS B 129 5 5 HELIX 14 14 ASP B 132 LEU B 143 1 12 HELIX 15 15 ASN B 157 MET B 173 1 17 SHEET 1 A 6 VAL A 43 LEU A 52 0 SHEET 2 A 6 LYS A 55 THR A 64 -1 O LEU A 59 N ARG A 48 SHEET 3 A 6 TYR A 7 GLY A 15 1 N TYR A 7 O LYS A 58 SHEET 4 A 6 GLY A 83 ASP A 89 1 O ILE A 85 N LEU A 12 SHEET 5 A 6 ASN A 115 ASN A 121 1 O ASN A 121 N TYR A 88 SHEET 6 A 6 PHE A 147 GLU A 149 1 O LEU A 148 N LEU A 118 SHEET 1 B 6 VAL B 43 LEU B 52 0 SHEET 2 B 6 LYS B 55 THR B 64 -1 O ASP B 63 N ASP B 44 SHEET 3 B 6 TYR B 7 GLY B 15 1 N LEU B 11 O TRP B 62 SHEET 4 B 6 GLY B 83 ASP B 89 1 O ILE B 85 N LEU B 12 SHEET 5 B 6 ASN B 115 ASN B 121 1 O ASN B 121 N TYR B 88 SHEET 6 B 6 PHE B 147 THR B 150 1 O THR B 150 N GLY B 120 LINK O2G GNP A 400 MG MG A 500 1555 1555 1.99 LINK OG SER B 22 MG MG B 500 1555 1555 2.05 LINK O2G GNP B 400 MG MG B 500 1555 1555 2.03 LINK O2B GNP A 400 MG MG A 500 1555 1555 2.05 LINK MG MG B 500 O HOH B 185 1555 1555 2.03 LINK MG MG A 500 O HOH A 218 1555 1555 2.08 LINK MG MG B 500 O HOH B 199 1555 1555 2.06 LINK MG MG A 500 O HOH A 189 1555 1555 2.05 LINK OG SER A 22 MG MG A 500 1555 1555 2.07 LINK OG1 THR A 40 MG MG A 500 1555 1555 2.08 LINK OG1 THR B 40 MG MG B 500 1555 1555 2.13 LINK O2B GNP B 400 MG MG B 500 1555 1555 2.09 LINK BA BA B 175 O HOH B 187 1555 1555 2.59 LINK BA BA A 175 O HOH A 261 1555 1555 2.65 LINK BA BA B 175 O HOH B 301 1555 1555 2.55 LINK OG1 THR B 134 BA BA B 175 1555 1555 2.72 LINK OD2 ASP B 132 BA BA B 175 1555 1555 2.83 LINK O VAL A 43 BA BA A 175 1555 1555 2.89 LINK OD1 ASP A 44 BA BA A 175 1555 1555 2.89 LINK BA BA B 175 O HOH B 228 1555 1555 2.85 LINK O ILE A 41 BA BA A 175 1555 1555 2.89 LINK OD1 ASP B 132 BA BA B 175 1555 1555 2.87 LINK OH TYR A 77 P AMP A 600 1555 1555 1.60 LINK OH TYR B 77 P AMP B 600 1555 1555 1.57 SITE 1 AC1 29 SER A 17 GLY A 18 VAL A 19 GLY A 20 SITE 2 AC1 29 LYS A 21 SER A 22 CYS A 23 TYR A 33 SITE 3 AC1 29 THR A 34 GLU A 35 SER A 36 SER A 39 SITE 4 AC1 29 THR A 40 GLY A 66 ASN A 121 LYS A 122 SITE 5 AC1 29 ASP A 124 LEU A 125 SER A 151 ALA A 152 SITE 6 AC1 29 LYS A 153 HOH A 187 HOH A 189 HOH A 191 SITE 7 AC1 29 HOH A 208 HOH A 211 HOH A 218 HOH A 291 SITE 8 AC1 29 MG A 500 SITE 1 AC2 5 SER A 22 THR A 40 HOH A 189 HOH A 218 SITE 2 AC2 5 GNP A 400 SITE 1 AC3 4 ILE A 41 VAL A 43 ASP A 44 HOH A 261 SITE 1 AC4 6 VAL A 43 PHE A 45 GLN A 60 TRP A 62 SITE 2 AC4 6 TYR A 77 HOH A 281 SITE 1 AC5 27 SER B 17 GLY B 18 VAL B 19 GLY B 20 SITE 2 AC5 27 LYS B 21 SER B 22 CYS B 23 TYR B 33 SITE 3 AC5 27 GLU B 35 THR B 40 GLY B 66 ASN B 121 SITE 4 AC5 27 LYS B 122 ASP B 124 LEU B 125 SER B 151 SITE 5 AC5 27 ALA B 152 LYS B 153 HOH B 181 HOH B 185 SITE 6 AC5 27 HOH B 199 HOH B 204 HOH B 212 HOH B 215 SITE 7 AC5 27 HOH B 227 HOH B 278 MG B 500 SITE 1 AC6 5 SER B 22 THR B 40 HOH B 185 HOH B 199 SITE 2 AC6 5 GNP B 400 SITE 1 AC7 8 GLU A 4 ASP A 6 THR A 56 ASP B 132 SITE 2 AC7 8 THR B 134 HOH B 187 HOH B 228 HOH B 301 SITE 1 AC8 6 PHE B 45 TRP B 62 TYR B 77 HOH B 176 SITE 2 AC8 6 HOH B 216 HOH B 256 CRYST1 34.970 100.589 45.071 90.00 102.43 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 0.028596 0.000000 0.006303 0.00000 SCALE2 0.000000 0.009941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022720 0.00000