HEADER HYDROLASE 03-JAN-19 6NJD TITLE CRYSTAL STRUCTURE OF RAVD (RESIDUES 1-200) FROM LEGIONELLA PNEUMOPHILA TITLE 2 (STRAIN CORBY) COMPLEXED WITH MET-1 LINKED DI-UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DI-UBIQUITIN; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RAVD; COMPND 7 CHAIN: B, D; COMPND 8 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: UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA; SOURCE 11 ORGANISM_TAXID: 446; SOURCE 12 STRAIN: CORBY; SOURCE 13 GENE: LPC_0242; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: B834(DE3) KEYWDS DEUBIQUITINASE, BACTERIAL EFFECTOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.WANG,Y.ZHOU,Y.ZHU REVDAT 4 08-JAN-20 6NJD 1 REMARK REVDAT 3 07-AUG-19 6NJD 1 JRNL REVDAT 2 05-JUN-19 6NJD 1 JRNL REVDAT 1 22-MAY-19 6NJD 0 JRNL AUTH M.WAN,X.WANG,C.HUANG,D.XU,Z.WANG,Y.ZHOU,Y.ZHU JRNL TITL A BACTERIAL EFFECTOR DEUBIQUITINASE SPECIFICALLY HYDROLYSES JRNL TITL 2 LINEAR UBIQUITIN CHAINS TO INHIBIT HOST INFLAMMATORY JRNL TITL 3 SIGNALLING. JRNL REF NAT MICROBIOL V. 4 1282 2019 JRNL REFN ESSN 2058-5276 JRNL PMID 31110362 JRNL DOI 10.1038/S41564-019-0454-1 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43764 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2331 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3178 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 186 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5234 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.17000 REMARK 3 B22 (A**2) : -2.71000 REMARK 3 B33 (A**2) : -1.46000 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): 0.223 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.182 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.162 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.912 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5325 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5135 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7193 ; 1.388 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11822 ; 0.894 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 660 ; 6.170 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 246 ;36.946 ;25.366 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 936 ;15.180 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;15.813 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 814 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6035 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1199 ; 0.002 ; 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 : 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 -4 A 148 REMARK 3 ORIGIN FOR THE GROUP (A): 27.0276 2.7486 24.5636 REMARK 3 T TENSOR REMARK 3 T11: 0.1677 T22: 0.0966 REMARK 3 T33: 0.2651 T12: -0.0875 REMARK 3 T13: 0.0390 T23: -0.0519 REMARK 3 L TENSOR REMARK 3 L11: 0.5470 L22: 1.4449 REMARK 3 L33: 1.3225 L12: -0.7955 REMARK 3 L13: -0.1950 L23: -0.2545 REMARK 3 S TENSOR REMARK 3 S11: 0.1090 S12: -0.0974 S13: -0.0515 REMARK 3 S21: -0.1098 S22: 0.2154 S23: 0.1267 REMARK 3 S31: -0.2133 S32: -0.0136 S33: -0.3244 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 8 B 198 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0749 9.4588 35.6674 REMARK 3 T TENSOR REMARK 3 T11: 0.0340 T22: 0.1180 REMARK 3 T33: 0.1407 T12: -0.0469 REMARK 3 T13: 0.0453 T23: -0.0244 REMARK 3 L TENSOR REMARK 3 L11: 0.5851 L22: 0.4651 REMARK 3 L33: 1.9943 L12: -0.0700 REMARK 3 L13: -0.0166 L23: 0.5724 REMARK 3 S TENSOR REMARK 3 S11: -0.0725 S12: 0.0049 S13: -0.0747 REMARK 3 S21: 0.0068 S22: -0.0690 S23: -0.0689 REMARK 3 S31: 0.0458 S32: -0.1618 S33: 0.1415 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 1 C 148 REMARK 3 ORIGIN FOR THE GROUP (A): 28.5633 52.1827 22.7534 REMARK 3 T TENSOR REMARK 3 T11: 0.2634 T22: 0.1170 REMARK 3 T33: 0.1061 T12: -0.0172 REMARK 3 T13: -0.0883 T23: 0.0489 REMARK 3 L TENSOR REMARK 3 L11: 0.6121 L22: 0.7262 REMARK 3 L33: 0.1475 L12: 0.5031 REMARK 3 L13: 0.1572 L23: 0.0297 REMARK 3 S TENSOR REMARK 3 S11: -0.1974 S12: 0.1134 S13: 0.2067 REMARK 3 S21: -0.0275 S22: 0.1157 S23: 0.1039 REMARK 3 S31: 0.0099 S32: 0.0440 S33: 0.0817 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 12 D 194 REMARK 3 ORIGIN FOR THE GROUP (A): 17.7296 46.6639 10.5870 REMARK 3 T TENSOR REMARK 3 T11: 0.0844 T22: 0.3515 REMARK 3 T33: 0.0557 T12: -0.0105 REMARK 3 T13: -0.0172 T23: 0.0713 REMARK 3 L TENSOR REMARK 3 L11: 0.1769 L22: 1.2139 REMARK 3 L33: 3.0646 L12: -0.4237 REMARK 3 L13: 0.7168 L23: -1.8118 REMARK 3 S TENSOR REMARK 3 S11: -0.0074 S12: -0.0378 S13: 0.0446 REMARK 3 S21: -0.0721 S22: -0.1085 S23: -0.1133 REMARK 3 S31: 0.1071 S32: -0.1979 S33: 0.1158 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 6NJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000238809. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-17 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97736 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87704 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.975 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.03 REMARK 200 R MERGE FOR SHELL (I) : 0.56800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, PH 8.5, 200 MM REMARK 280 MAGNESIUM CHLORIDE AND 20% PEG3350, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 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 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 38.87000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.04500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.87000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.04500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 LEU A 149 REMARK 465 ARG A 150 REMARK 465 GLY A 151 REMARK 465 GLY A 152 REMARK 465 GLY B -4 REMARK 465 PRO B -3 REMARK 465 LEU B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MSE B 1 REMARK 465 ASN B 2 REMARK 465 LEU B 3 REMARK 465 LYS B 4 REMARK 465 ALA B 5 REMARK 465 GLU B 6 REMARK 465 VAL B 7 REMARK 465 ALA B 199 REMARK 465 GLU B 200 REMARK 465 GLY C -4 REMARK 465 PRO C -3 REMARK 465 LEU C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 ILE C 3 REMARK 465 PHE C 4 REMARK 465 ILE C 13 REMARK 465 GLU C 16 REMARK 465 LYS C 63 REMARK 465 GLU C 64 REMARK 465 SER C 65 REMARK 465 LEU C 149 REMARK 465 ARG C 150 REMARK 465 GLY C 151 REMARK 465 GLY C 152 REMARK 465 GLY D -4 REMARK 465 PRO D -3 REMARK 465 LEU D -2 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 MSE D 1 REMARK 465 ASN D 2 REMARK 465 LEU D 3 REMARK 465 LYS D 4 REMARK 465 ALA D 5 REMARK 465 GLU D 6 REMARK 465 VAL D 7 REMARK 465 PHE D 8 REMARK 465 LEU D 9 REMARK 465 ASN D 10 REMARK 465 GLN D 11 REMARK 465 ALA D 195 REMARK 465 ARG D 196 REMARK 465 ALA D 197 REMARK 465 LYS D 198 REMARK 465 ALA D 199 REMARK 465 GLU D 200 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 GLU A 16 CG CD OE1 OE2 REMARK 470 GLN C 2 CG CD OE1 NE2 REMARK 470 LEU C 8 CG CD1 CD2 REMARK 470 THR C 14 OG1 CG2 REMARK 470 GLU C 18 CG CD OE1 OE2 REMARK 470 ASN C 25 CG OD1 ND2 REMARK 470 VAL C 26 CG1 CG2 REMARK 470 ILE C 61 CG1 CG2 CD1 REMARK 470 GLN C 62 CG CD OE1 NE2 REMARK 470 GLU C 100 CG CD OE1 OE2 REMARK 470 ARG D 36 CG CD NE CZ NH1 NH2 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 LEU B 9 64.23 63.23 REMARK 500 GLN B 11 62.61 -100.20 REMARK 500 GLN B 172 -97.65 -135.04 REMARK 500 ASN C 60 58.63 38.28 REMARK 500 GLN D 172 -109.12 -133.91 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 108 OD1 REMARK 620 2 HOH A 316 O 87.6 REMARK 620 3 HOH A 307 O 89.6 95.6 REMARK 620 4 HOH D 355 O 178.4 93.9 90.9 REMARK 620 5 HOH D 314 O 92.4 172.4 91.9 86.0 REMARK 620 N 1 2 3 4 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 GLU B 186 OE2 REMARK 620 2 HOH B 481 O 91.3 REMARK 620 3 ASP C 108 OD1 46.0 45.3 REMARK 620 4 HOH C 224 O 154.2 79.6 120.8 REMARK 620 5 HOH C 243 O 119.8 100.6 118.7 85.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 301 DBREF 6NJD A 1 152 UNP F5H747 F5H747_HUMAN 1 152 DBREF 6NJD B -4 200 PDB 6NJD 6NJD -4 200 DBREF 6NJD C 1 152 UNP F5H747 F5H747_HUMAN 1 152 DBREF 6NJD D -4 200 PDB 6NJD 6NJD -4 200 SEQADV 6NJD GLY A -4 UNP F5H747 EXPRESSION TAG SEQADV 6NJD PRO A -3 UNP F5H747 EXPRESSION TAG SEQADV 6NJD LEU A -2 UNP F5H747 EXPRESSION TAG SEQADV 6NJD GLY A -1 UNP F5H747 EXPRESSION TAG SEQADV 6NJD SER A 0 UNP F5H747 EXPRESSION TAG SEQADV 6NJD SER A 75 UNP F5H747 GLY 75 ENGINEERED MUTATION SEQADV 6NJD SER A 76 UNP F5H747 GLY 76 ENGINEERED MUTATION SEQADV 6NJD GLY C -4 UNP F5H747 EXPRESSION TAG SEQADV 6NJD PRO C -3 UNP F5H747 EXPRESSION TAG SEQADV 6NJD LEU C -2 UNP F5H747 EXPRESSION TAG SEQADV 6NJD GLY C -1 UNP F5H747 EXPRESSION TAG SEQADV 6NJD SER C 0 UNP F5H747 EXPRESSION TAG SEQADV 6NJD SER C 75 UNP F5H747 GLY 75 ENGINEERED MUTATION SEQADV 6NJD SER C 76 UNP F5H747 GLY 76 ENGINEERED MUTATION SEQRES 1 A 157 GLY PRO LEU GLY SER MET GLN ILE PHE VAL LYS THR LEU SEQRES 2 A 157 THR GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP SEQRES 3 A 157 THR ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU SEQRES 4 A 157 GLY ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY SEQRES 5 A 157 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN SEQRES 6 A 157 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU SEQRES 7 A 157 ARG SER SER MET GLN ILE PHE VAL LYS THR LEU THR GLY SEQRES 8 A 157 LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE SEQRES 9 A 157 GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE SEQRES 10 A 157 PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN SEQRES 11 A 157 LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN SEQRES 12 A 157 LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY SEQRES 13 A 157 GLY SEQRES 1 B 205 GLY PRO LEU GLY SER MSE ASN LEU LYS ALA GLU VAL PHE SEQRES 2 B 205 LEU ASN GLN ASN CYS ALA GLU MSE MSE ILE LYS LYS ALA SEQRES 3 B 205 ALA GLN LEU ILE LEU GLY SER ASP LEU ASP PHE GLU TYR SEQRES 4 B 205 THR ARG GLY ILE GLN ASP ILE GLN VAL ASP LEU GLY PRO SEQRES 5 B 205 ALA PHE MSE PHE SER PRO ASP GLU GLU LYS THR LEU TRP SEQRES 6 B 205 VAL SER GLY LYS ASN GLN GLU THR LEU GLU LYS ASP LEU SEQRES 7 B 205 ALA THR LEU ASN LYS SER SER VAL TYR PHE PHE ARG THR SEQRES 8 B 205 GLY THR GLN GLY GLY ALA GLY HIS TRP GLN VAL LEU TYR SEQRES 9 B 205 TYR GLU ALA ALA LYS SER GLY TRP VAL SER TYR SER SER SEQRES 10 B 205 GLN SER ASN HIS PHE GLN VAL THR ASP SER ASN GLY LYS SEQRES 11 B 205 LEU THR ALA SER GLY LYS GLY LEU LEU VAL PRO HIS ALA SEQRES 12 B 205 ASN TRP GLY LYS GLU ASN GLY ASN TYR ALA PHE LEU LEU SEQRES 13 B 205 VAL ASN ALA SER ALA GLU ASN ILE ILE HIS ALA ALA ASN SEQRES 14 B 205 PHE VAL TYR ILE LEU ARG THR GLN ASN GLU VAL ALA ALA SEQRES 15 B 205 ILE GLU TYR CYS ALA LEU ASN HIS GLU PHE HIS PRO GLU SEQRES 16 B 205 ILE LYS ARG THR ALA ARG ALA LYS ALA GLU SEQRES 1 C 157 GLY PRO LEU GLY SER MET GLN ILE PHE VAL LYS THR LEU SEQRES 2 C 157 THR GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP SEQRES 3 C 157 THR ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU SEQRES 4 C 157 GLY ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY SEQRES 5 C 157 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN SEQRES 6 C 157 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU SEQRES 7 C 157 ARG SER SER MET GLN ILE PHE VAL LYS THR LEU THR GLY SEQRES 8 C 157 LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE SEQRES 9 C 157 GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE SEQRES 10 C 157 PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN SEQRES 11 C 157 LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN SEQRES 12 C 157 LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY SEQRES 13 C 157 GLY SEQRES 1 D 205 GLY PRO LEU GLY SER MSE ASN LEU LYS ALA GLU VAL PHE SEQRES 2 D 205 LEU ASN GLN ASN CYS ALA GLU MSE MSE ILE LYS LYS ALA SEQRES 3 D 205 ALA GLN LEU ILE LEU GLY SER ASP LEU ASP PHE GLU TYR SEQRES 4 D 205 THR ARG GLY ILE GLN ASP ILE GLN VAL ASP LEU GLY PRO SEQRES 5 D 205 ALA PHE MSE PHE SER PRO ASP GLU GLU LYS THR LEU TRP SEQRES 6 D 205 VAL SER GLY LYS ASN GLN GLU THR LEU GLU LYS ASP LEU SEQRES 7 D 205 ALA THR LEU ASN LYS SER SER VAL TYR PHE PHE ARG THR SEQRES 8 D 205 GLY THR GLN GLY GLY ALA GLY HIS TRP GLN VAL LEU TYR SEQRES 9 D 205 TYR GLU ALA ALA LYS SER GLY TRP VAL SER TYR SER SER SEQRES 10 D 205 GLN SER ASN HIS PHE GLN VAL THR ASP SER ASN GLY LYS SEQRES 11 D 205 LEU THR ALA SER GLY LYS GLY LEU LEU VAL PRO HIS ALA SEQRES 12 D 205 ASN TRP GLY LYS GLU ASN GLY ASN TYR ALA PHE LEU LEU SEQRES 13 D 205 VAL ASN ALA SER ALA GLU ASN ILE ILE HIS ALA ALA ASN SEQRES 14 D 205 PHE VAL TYR ILE LEU ARG THR GLN ASN GLU VAL ALA ALA SEQRES 15 D 205 ILE GLU TYR CYS ALA LEU ASN HIS GLU PHE HIS PRO GLU SEQRES 16 D 205 ILE LYS ARG THR ALA ARG ALA LYS ALA GLU HET MSE B 16 8 HET MSE B 17 8 HET MSE B 50 8 HET MSE D 16 8 HET MSE D 17 8 HET MSE D 50 8 HET MG A 201 1 HET MG B 301 1 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION FORMUL 2 MSE 6(C5 H11 N O2 SE) FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *275(H2 O) HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 ASP A 39 5 3 HELIX 3 AA3 LEU A 56 ASN A 60 5 5 HELIX 4 AA4 THR A 98 GLY A 111 1 14 HELIX 5 AA5 PRO A 113 ASP A 115 5 3 HELIX 6 AA6 LEU A 132 ASN A 136 5 5 HELIX 7 AA7 ASN B 12 GLY B 27 1 16 HELIX 8 AA8 LEU B 45 MSE B 50 5 6 HELIX 9 AA9 PRO B 53 GLU B 55 5 3 HELIX 10 AB1 ASN B 65 THR B 75 1 11 HELIX 11 AB2 THR B 127 GLY B 132 1 6 HELIX 12 AB3 SER B 155 GLN B 172 1 18 HELIX 13 AB4 ASN B 173 ASN B 184 1 12 HELIX 14 AB5 THR C 22 GLY C 35 1 14 HELIX 15 AB6 PRO C 37 ASP C 39 5 3 HELIX 16 AB7 THR C 98 GLY C 111 1 14 HELIX 17 AB8 PRO C 113 ASP C 115 5 3 HELIX 18 AB9 LEU C 132 ASN C 136 5 5 HELIX 19 AC1 CYS D 13 GLY D 27 1 15 HELIX 20 AC2 LEU D 45 MSE D 50 5 6 HELIX 21 AC3 PRO D 53 GLU D 55 5 3 HELIX 22 AC4 ASN D 65 THR D 75 1 11 HELIX 23 AC5 THR D 127 GLY D 132 1 6 HELIX 24 AC6 SER D 155 GLN D 172 1 18 HELIX 25 AC7 ASN D 173 ASN D 184 1 12 SHEET 1 AA1 5 THR A 12 VAL A 17 0 SHEET 2 AA1 5 MET A 1 LYS A 6 -1 N MET A 1 O VAL A 17 SHEET 3 AA1 5 THR A 66 LEU A 71 1 O LEU A 69 N LYS A 6 SHEET 4 AA1 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 AA1 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 AA2 5 THR A 88 VAL A 93 0 SHEET 2 AA2 5 MET A 77 THR A 83 -1 N MET A 77 O VAL A 93 SHEET 3 AA2 5 THR A 142 LEU A 147 1 O LEU A 143 N PHE A 80 SHEET 4 AA2 5 GLN A 117 PHE A 121 -1 N ARG A 118 O VAL A 146 SHEET 5 AA2 5 LYS A 124 GLN A 125 -1 O LYS A 124 N PHE A 121 SHEET 1 AA3 2 SER B 28 PHE B 32 0 SHEET 2 AA3 2 ILE B 191 ALA B 195 -1 O THR B 194 N ASP B 29 SHEET 1 AA4 6 LYS B 57 TRP B 60 0 SHEET 2 AA4 6 TYR B 147 ASN B 153 -1 O PHE B 149 N TRP B 60 SHEET 3 AA4 6 TYR B 82 THR B 88 -1 N PHE B 83 O VAL B 152 SHEET 4 AA4 6 GLY B 93 TYR B 100 -1 O LEU B 98 N TYR B 82 SHEET 5 AA4 6 TRP B 107 SER B 112 -1 O TYR B 110 N VAL B 97 SHEET 6 AA4 6 ASN B 115 GLN B 118 -1 O PHE B 117 N SER B 109 SHEET 1 AA5 3 LYS C 48 GLN C 49 0 SHEET 2 AA5 3 GLN C 41 PHE C 45 -1 N PHE C 45 O LYS C 48 SHEET 3 AA5 3 HIS C 68 LEU C 71 -1 O HIS C 68 N ILE C 44 SHEET 1 AA6 5 THR C 88 VAL C 93 0 SHEET 2 AA6 5 MET C 77 LYS C 82 -1 N MET C 77 O VAL C 93 SHEET 3 AA6 5 THR C 142 LEU C 147 1 O LEU C 145 N LYS C 82 SHEET 4 AA6 5 GLN C 117 PHE C 121 -1 N ARG C 118 O VAL C 146 SHEET 5 AA6 5 LYS C 124 GLN C 125 -1 O LYS C 124 N PHE C 121 SHEET 1 AA7 2 LEU D 30 PHE D 32 0 SHEET 2 AA7 2 ILE D 191 ARG D 193 -1 O LYS D 192 N ASP D 31 SHEET 1 AA8 6 LYS D 57 TRP D 60 0 SHEET 2 AA8 6 PHE D 149 ASN D 153 -1 O LEU D 151 N THR D 58 SHEET 3 AA8 6 TYR D 82 GLY D 87 -1 N PHE D 83 O VAL D 152 SHEET 4 AA8 6 GLY D 93 GLU D 101 -1 O LEU D 98 N TYR D 82 SHEET 5 AA8 6 GLY D 106 SER D 112 -1 O TYR D 110 N VAL D 97 SHEET 6 AA8 6 ASN D 115 GLN D 118 -1 O PHE D 117 N SER D 109 LINK OD1 ASP A 108 MG MG A 201 1555 1555 2.19 LINK C GLU B 15 N MSE B 16 1555 1555 1.33 LINK C MSE B 16 N MSE B 17 1555 1555 1.32 LINK C MSE B 17 N ILE B 18 1555 1555 1.32 LINK C PHE B 49 N MSE B 50 1555 1555 1.33 LINK C MSE B 50 N PHE B 51 1555 1555 1.33 LINK OE2 GLU B 186 MG MG B 301 1555 1555 2.37 LINK C GLU D 15 N MSE D 16 1555 1555 1.34 LINK C MSE D 16 N MSE D 17 1555 1555 1.33 LINK C MSE D 17 N ILE D 18 1555 1555 1.33 LINK C PHE D 49 N MSE D 50 1555 1555 1.33 LINK C MSE D 50 N PHE D 51 1555 1555 1.34 LINK MG MG A 201 O HOH A 316 1555 1555 2.12 LINK MG MG A 201 O HOH A 307 1555 1555 1.98 LINK MG MG B 301 O HOH B 481 1555 1555 2.20 LINK OD1 ASP C 108 MG MG B 301 1555 3556 2.31 LINK MG MG A 201 O HOH D 355 1555 3545 2.06 LINK MG MG A 201 O HOH D 314 1555 3545 2.07 LINK MG MG B 301 O HOH C 224 1555 3546 2.22 LINK MG MG B 301 O HOH C 243 1555 3546 1.93 SITE 1 AC1 6 ASP A 108 HOH A 307 HOH A 316 HIS D 185 SITE 2 AC1 6 HOH D 314 HOH D 355 SITE 1 AC2 6 HIS B 185 GLU B 186 HOH B 481 ASP C 108 SITE 2 AC2 6 HOH C 224 HOH C 243 CRYST1 77.740 102.090 90.920 90.00 90.00 90.00 P 21 21 2 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 0.012863 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009795 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010999 0.00000