HEADER TRANSFERASE 28-JUN-07 2JII TITLE STRUCTURE OF VACCINIA RELATED KINASE 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE VRK3 MOLECULE: VACCINIA COMPND 3 RELATED KINASE 3; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: KINASE DOMAIN, RESIDUES 146-474; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: R3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS TRANSFERASE, PSEUDO KINASE DOMAIN, VACCINIA RELATED KINASE, KEYWDS 2 SERINE/THREONINE-PROTEIN KINASE, VRK3, KINASE, ATP-BINDING, KEYWDS 3 NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.BUNKOCZI,J.ESWARAN,A.C.W.PIKE,J.UPPENBERG,E.UGOCHUKWU,F.VON DELFT, AUTHOR 2 C.COOPER,E.SALAH,P.SAVITSKY,N.BURGESS-BROWN,T.KEATES,O.FEDOROV, AUTHOR 3 F.SOBOTT,C.H.ARROWSMITH,A.EDWARDS,M.SUNDSTROM,J.WEIGELT,S.KNAPP REVDAT 6 01-MAY-24 2JII 1 REMARK REVDAT 5 28-FEB-18 2JII 1 SOURCE JRNL REVDAT 4 13-JUL-11 2JII 1 VERSN REVDAT 3 04-AUG-09 2JII 1 JRNL REMARK REVDAT 2 24-FEB-09 2JII 1 VERSN REVDAT 1 10-JUL-07 2JII 0 JRNL AUTH E.D.SCHEEFF,J.ESWARAN,G.BUNKOCZI,S.KNAPP,G.MANNING JRNL TITL STRUCTURE OF THE PSEUDOKINASE VRK3 REVEALS A DEGRADED JRNL TITL 2 CATALYTIC SITE, A HIGHLY CONSERVED KINASE FOLD, AND A JRNL TITL 3 PUTATIVE REGULATORY BINDING SITE. JRNL REF STRUCTURE V. 17 128 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19141289 JRNL DOI 10.1016/J.STR.2008.10.018 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0034 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 57853 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3092 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4009 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE SET COUNT : 237 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5111 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 514 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : -1.27000 REMARK 3 B33 (A**2) : 1.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.27000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.147 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.389 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5294 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3639 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7181 ; 1.265 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8867 ; 0.930 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 643 ; 5.975 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 244 ;31.591 ;24.098 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 873 ;13.809 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;17.843 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 777 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5850 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1069 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1104 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3734 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2530 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2632 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 388 ; 0.164 ; 0.200 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): 12 ; 0.134 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 58 ; 0.201 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.114 ; 0.200 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): 3326 ; 3.047 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5227 ; 4.014 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2246 ; 6.364 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1954 ; 7.950 ;11.000 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 141 A 472 5 REMARK 3 1 B 141 B 472 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1882 ; 0.23 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 2406 ; 0.50 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1882 ; 0.81 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 2406 ; 0.88 ; 10.00 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 141 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 66.9542 29.2297 48.3790 REMARK 3 T TENSOR REMARK 3 T11: -0.1003 T22: -0.0373 REMARK 3 T33: 0.1132 T12: -0.0010 REMARK 3 T13: -0.0105 T23: 0.0193 REMARK 3 L TENSOR REMARK 3 L11: 0.5613 L22: 2.7109 REMARK 3 L33: 0.7511 L12: -0.5987 REMARK 3 L13: -0.1247 L23: 0.7437 REMARK 3 S TENSOR REMARK 3 S11: -0.0239 S12: -0.0983 S13: 0.3398 REMARK 3 S21: 0.0711 S22: 0.1744 S23: -0.0326 REMARK 3 S31: -0.0438 S32: 0.0708 S33: -0.1505 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 : A 263 A 472 REMARK 3 ORIGIN FOR THE GROUP (A): 59.6927 8.6512 39.7750 REMARK 3 T TENSOR REMARK 3 T11: -0.1233 T22: -0.0744 REMARK 3 T33: -0.0366 T12: 0.0049 REMARK 3 T13: 0.0076 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 2.9253 L22: 2.0206 REMARK 3 L33: 0.8504 L12: -0.0584 REMARK 3 L13: -0.0814 L23: 0.0795 REMARK 3 S TENSOR REMARK 3 S11: -0.0240 S12: 0.2177 S13: -0.2349 REMARK 3 S21: 0.0240 S22: 0.0277 S23: 0.1220 REMARK 3 S31: 0.0802 S32: -0.0800 S33: -0.0038 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 : B 137 B 262 REMARK 3 ORIGIN FOR THE GROUP (A): 86.5170 16.2967 21.6835 REMARK 3 T TENSOR REMARK 3 T11: -0.0682 T22: -0.1115 REMARK 3 T33: -0.1100 T12: 0.0026 REMARK 3 T13: 0.0233 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 1.0161 L22: 2.0203 REMARK 3 L33: 2.2126 L12: 0.0779 REMARK 3 L13: 0.0936 L23: -0.5399 REMARK 3 S TENSOR REMARK 3 S11: 0.0013 S12: 0.0150 S13: -0.0188 REMARK 3 S21: -0.0394 S22: 0.1156 S23: -0.0004 REMARK 3 S31: -0.0247 S32: -0.0294 S33: -0.1168 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 : B 263 B 472 REMARK 3 ORIGIN FOR THE GROUP (A): 95.9627 -4.0206 15.6224 REMARK 3 T TENSOR REMARK 3 T11: -0.0613 T22: -0.1221 REMARK 3 T33: -0.1297 T12: 0.0007 REMARK 3 T13: -0.0091 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 1.0816 L22: 1.7656 REMARK 3 L33: 1.8008 L12: -0.2543 REMARK 3 L13: -0.3671 L23: 0.2135 REMARK 3 S TENSOR REMARK 3 S11: -0.0081 S12: -0.0003 S13: 0.0686 REMARK 3 S21: -0.0132 S22: 0.0561 S23: -0.1012 REMARK 3 S31: 0.0702 S32: 0.1358 S33: -0.0480 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2JII COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1290033070. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 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) : 1.0331 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60969 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: ENSEMBLE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH=7.5 2.0 M REMARK 280 AMMONIUMFORMATE, PH 7.50 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 27.21150 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: PQS 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: PQS 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 123 REMARK 465 HIS A 124 REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 SER A 130 REMARK 465 SER A 131 REMARK 465 GLY A 132 REMARK 465 VAL A 133 REMARK 465 ASP A 134 REMARK 465 LEU A 135 REMARK 465 GLY A 136 REMARK 465 THR A 137 REMARK 465 GLU A 138 REMARK 465 ASN A 139 REMARK 465 LEU A 140 REMARK 465 THR A 188 REMARK 465 LEU A 189 REMARK 465 THR A 190 REMARK 465 CYS A 191 REMARK 465 ASP A 192 REMARK 465 SER A 193 REMARK 465 GLY A 194 REMARK 465 PRO A 195 REMARK 465 GLN A 196 REMARK 465 LYS A 197 REMARK 465 GLN A 198 REMARK 465 VAL A 473 REMARK 465 PRO A 474 REMARK 465 MET B 123 REMARK 465 HIS B 124 REMARK 465 HIS B 125 REMARK 465 HIS B 126 REMARK 465 HIS B 127 REMARK 465 HIS B 128 REMARK 465 HIS B 129 REMARK 465 SER B 130 REMARK 465 SER B 131 REMARK 465 GLY B 132 REMARK 465 VAL B 133 REMARK 465 ASP B 134 REMARK 465 LEU B 135 REMARK 465 GLY B 136 REMARK 465 THR B 188 REMARK 465 LEU B 189 REMARK 465 THR B 190 REMARK 465 CYS B 191 REMARK 465 ASP B 192 REMARK 465 SER B 193 REMARK 465 GLY B 194 REMARK 465 PRO B 195 REMARK 465 GLN B 196 REMARK 465 LYS B 197 REMARK 465 VAL B 473 REMARK 465 PRO B 474 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 LYS A 199 CG CD CE NZ REMARK 470 LYS A 229 CE NZ REMARK 470 LYS A 232 CD CE NZ REMARK 470 LYS A 253 CE NZ REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 LYS A 338 CG CD CE NZ REMARK 470 LYS A 406 CE NZ REMARK 470 LYS A 410 CD CE NZ REMARK 470 LYS A 433 CE NZ REMARK 470 ARG A 461 CD NE CZ NH1 NH2 REMARK 470 MET A 472 CG SD CE REMARK 470 THR B 137 OG1 CG2 REMARK 470 GLU B 138 CG CD OE1 OE2 REMARK 470 LEU B 140 CG CD1 CD2 REMARK 470 LYS B 169 CD CE NZ REMARK 470 GLN B 198 CG CD OE1 NE2 REMARK 470 LYS B 199 CG CD CE NZ REMARK 470 LYS B 232 CG CD CE NZ REMARK 470 LYS B 275 CG CD CE NZ REMARK 470 LYS B 338 CG CD CE NZ 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 GLN A 172 -70.59 -113.99 REMARK 500 ASP A 175 -155.90 -156.75 REMARK 500 ASP A 252 17.93 58.30 REMARK 500 GLU A 301 3.01 80.39 REMARK 500 ASN A 306 56.03 -157.36 REMARK 500 ASP A 318 93.78 -165.87 REMARK 500 ALA A 325 -158.76 -126.84 REMARK 500 LYS A 410 85.09 -156.03 REMARK 500 GLN B 172 -70.44 -105.38 REMARK 500 THR B 236 66.82 -117.63 REMARK 500 LEU B 239 133.33 -39.09 REMARK 500 ASN B 306 61.11 -154.82 REMARK 500 ASP B 318 88.16 -158.61 REMARK 500 ALA B 325 -160.08 -126.23 REMARK 500 LYS B 410 83.27 -152.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2087 DISTANCE = 6.69 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1473 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1474 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1475 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1473 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1474 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 123-145 BELONG TO AN UNCLEAVED HIS-TAG DBREF 2JII A 123 145 PDB 2JII 2JII 123 145 DBREF 2JII A 146 474 UNP Q8IV63 VRK3_HUMAN 146 474 DBREF 2JII B 123 145 PDB 2JII 2JII 123 145 DBREF 2JII B 146 474 UNP Q8IV63 VRK3_HUMAN 146 474 SEQRES 1 A 352 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 352 GLY THR GLU ASN LEU TYR PHE GLN SER MET THR THR SER SEQRES 3 A 352 LEU GLU ALA LEU PRO THR GLY THR VAL LEU THR ASP LYS SEQRES 4 A 352 SER GLY ARG GLN TRP LYS LEU LYS SER PHE GLN THR ARG SEQRES 5 A 352 ASP ASN GLN GLY ILE LEU TYR GLU ALA ALA PRO THR SER SEQRES 6 A 352 THR LEU THR CYS ASP SER GLY PRO GLN LYS GLN LYS PHE SEQRES 7 A 352 SER LEU LYS LEU ASP ALA LYS ASP GLY ARG LEU PHE ASN SEQRES 8 A 352 GLU GLN ASN PHE PHE GLN ARG ALA ALA LYS PRO LEU GLN SEQRES 9 A 352 VAL ASN LYS TRP LYS LYS LEU TYR SER THR PRO LEU LEU SEQRES 10 A 352 ALA ILE PRO THR CYS MET GLY PHE GLY VAL HIS GLN ASP SEQRES 11 A 352 LYS TYR ARG PHE LEU VAL LEU PRO SER LEU GLY ARG SER SEQRES 12 A 352 LEU GLN SER ALA LEU ASP VAL SER PRO LYS HIS VAL LEU SEQRES 13 A 352 SER GLU ARG SER VAL LEU GLN VAL ALA CYS ARG LEU LEU SEQRES 14 A 352 ASP ALA LEU GLU PHE LEU HIS GLU ASN GLU TYR VAL HIS SEQRES 15 A 352 GLY ASN VAL THR ALA GLU ASN ILE PHE VAL ASP PRO GLU SEQRES 16 A 352 ASP GLN SER GLN VAL THR LEU ALA GLY TYR GLY PHE ALA SEQRES 17 A 352 PHE ARG TYR CYS PRO SER GLY LYS HIS VAL ALA TYR VAL SEQRES 18 A 352 GLU GLY SER ARG SER PRO HIS GLU GLY ASP LEU GLU PHE SEQRES 19 A 352 ILE SER MET ASP LEU HIS LYS GLY CYS GLY PRO SER ARG SEQRES 20 A 352 ARG SER ASP LEU GLN SER LEU GLY TYR CYS MET LEU LYS SEQRES 21 A 352 TRP LEU TYR GLY PHE LEU PRO TRP THR ASN CYS LEU PRO SEQRES 22 A 352 ASN THR GLU ASP ILE MET LYS GLN LYS GLN LYS PHE VAL SEQRES 23 A 352 ASP LYS PRO GLY PRO PHE VAL GLY PRO CYS GLY HIS TRP SEQRES 24 A 352 ILE ARG PRO SER GLU THR LEU GLN LYS TYR LEU LYS VAL SEQRES 25 A 352 VAL MET ALA LEU THR TYR GLU GLU LYS PRO PRO TYR ALA SEQRES 26 A 352 MET LEU ARG ASN ASN LEU GLU ALA LEU LEU GLN ASP LEU SEQRES 27 A 352 ARG VAL SER PRO TYR ASP PRO ILE GLY LEU PRO MET VAL SEQRES 28 A 352 PRO SEQRES 1 B 352 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 B 352 GLY THR GLU ASN LEU TYR PHE GLN SER MET THR THR SER SEQRES 3 B 352 LEU GLU ALA LEU PRO THR GLY THR VAL LEU THR ASP LYS SEQRES 4 B 352 SER GLY ARG GLN TRP LYS LEU LYS SER PHE GLN THR ARG SEQRES 5 B 352 ASP ASN GLN GLY ILE LEU TYR GLU ALA ALA PRO THR SER SEQRES 6 B 352 THR LEU THR CYS ASP SER GLY PRO GLN LYS GLN LYS PHE SEQRES 7 B 352 SER LEU LYS LEU ASP ALA LYS ASP GLY ARG LEU PHE ASN SEQRES 8 B 352 GLU GLN ASN PHE PHE GLN ARG ALA ALA LYS PRO LEU GLN SEQRES 9 B 352 VAL ASN LYS TRP LYS LYS LEU TYR SER THR PRO LEU LEU SEQRES 10 B 352 ALA ILE PRO THR CYS MET GLY PHE GLY VAL HIS GLN ASP SEQRES 11 B 352 LYS TYR ARG PHE LEU VAL LEU PRO SER LEU GLY ARG SER SEQRES 12 B 352 LEU GLN SER ALA LEU ASP VAL SER PRO LYS HIS VAL LEU SEQRES 13 B 352 SER GLU ARG SER VAL LEU GLN VAL ALA CYS ARG LEU LEU SEQRES 14 B 352 ASP ALA LEU GLU PHE LEU HIS GLU ASN GLU TYR VAL HIS SEQRES 15 B 352 GLY ASN VAL THR ALA GLU ASN ILE PHE VAL ASP PRO GLU SEQRES 16 B 352 ASP GLN SER GLN VAL THR LEU ALA GLY TYR GLY PHE ALA SEQRES 17 B 352 PHE ARG TYR CYS PRO SER GLY LYS HIS VAL ALA TYR VAL SEQRES 18 B 352 GLU GLY SER ARG SER PRO HIS GLU GLY ASP LEU GLU PHE SEQRES 19 B 352 ILE SER MET ASP LEU HIS LYS GLY CYS GLY PRO SER ARG SEQRES 20 B 352 ARG SER ASP LEU GLN SER LEU GLY TYR CYS MET LEU LYS SEQRES 21 B 352 TRP LEU TYR GLY PHE LEU PRO TRP THR ASN CYS LEU PRO SEQRES 22 B 352 ASN THR GLU ASP ILE MET LYS GLN LYS GLN LYS PHE VAL SEQRES 23 B 352 ASP LYS PRO GLY PRO PHE VAL GLY PRO CYS GLY HIS TRP SEQRES 24 B 352 ILE ARG PRO SER GLU THR LEU GLN LYS TYR LEU LYS VAL SEQRES 25 B 352 VAL MET ALA LEU THR TYR GLU GLU LYS PRO PRO TYR ALA SEQRES 26 B 352 MET LEU ARG ASN ASN LEU GLU ALA LEU LEU GLN ASP LEU SEQRES 27 B 352 ARG VAL SER PRO TYR ASP PRO ILE GLY LEU PRO MET VAL SEQRES 28 B 352 PRO HET EDO A1473 4 HET EDO A1474 4 HET EDO A1475 4 HET EDO B1473 4 HET EDO B1474 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 5(C2 H6 O2) FORMUL 8 HOH *514(H2 O) HELIX 1 1 TYR A 141 LEU A 149 1 9 HELIX 2 2 ARG A 210 ALA A 222 1 13 HELIX 3 3 LYS A 223 TYR A 234 1 12 HELIX 4 4 LEU A 266 SER A 273 1 8 HELIX 5 5 PRO A 274 VAL A 277 5 4 HELIX 6 6 SER A 279 ASN A 300 1 22 HELIX 7 7 GLY A 326 ALA A 330 5 5 HELIX 8 8 CYS A 334 LYS A 338 5 5 HELIX 9 9 SER A 358 LYS A 363 1 6 HELIX 10 10 SER A 368 GLY A 386 1 19 HELIX 11 11 TRP A 390 LEU A 394 5 5 HELIX 12 12 ASN A 396 LYS A 410 1 15 HELIX 13 13 SER A 425 ALA A 437 1 13 HELIX 14 14 PRO A 445 LEU A 460 1 16 HELIX 15 15 THR B 137 SER B 148 1 12 HELIX 16 16 ARG B 210 ALA B 222 1 13 HELIX 17 17 LYS B 223 SER B 235 1 13 HELIX 18 18 LEU B 266 VAL B 272 1 7 HELIX 19 19 SER B 273 VAL B 277 5 5 HELIX 20 20 SER B 279 ASN B 300 1 22 HELIX 21 21 GLY B 326 ALA B 330 5 5 HELIX 22 22 CYS B 334 LYS B 338 5 5 HELIX 23 23 SER B 358 LYS B 363 1 6 HELIX 24 24 SER B 368 GLY B 386 1 19 HELIX 25 25 TRP B 390 LEU B 394 5 5 HELIX 26 26 ASN B 396 LYS B 410 1 15 HELIX 27 27 SER B 425 ALA B 437 1 13 HELIX 28 28 PRO B 445 LEU B 460 1 16 SHEET 1 AA 6 VAL A 157 THR A 159 0 SHEET 2 AA 6 GLN A 165 ASP A 175 -1 O TRP A 166 N LEU A 158 SHEET 3 AA 6 GLY A 178 PRO A 185 -1 O GLY A 178 N ASP A 175 SHEET 4 AA 6 PHE A 200 ALA A 206 -1 O PHE A 200 N ALA A 183 SHEET 5 AA 6 TYR A 254 PRO A 260 -1 O ARG A 255 N ASP A 205 SHEET 6 AA 6 GLY A 246 HIS A 250 -1 O GLY A 246 N VAL A 258 SHEET 1 AB 3 ARG A 264 SER A 265 0 SHEET 2 AB 3 ILE A 312 ASP A 315 -1 O VAL A 314 N ARG A 264 SHEET 3 AB 3 ASP A 318 LEU A 324 -1 N ASP A 318 O ASP A 315 SHEET 1 AC 2 PHE A 414 VAL A 415 0 SHEET 2 AC 2 TRP A 421 ILE A 422 -1 O ILE A 422 N PHE A 414 SHEET 1 BA 6 VAL B 157 THR B 159 0 SHEET 2 BA 6 GLN B 165 ASP B 175 -1 O TRP B 166 N LEU B 158 SHEET 3 BA 6 GLY B 178 PRO B 185 -1 O GLY B 178 N ASP B 175 SHEET 4 BA 6 PHE B 200 ALA B 206 -1 O PHE B 200 N ALA B 183 SHEET 5 BA 6 TYR B 254 PRO B 260 -1 O ARG B 255 N ASP B 205 SHEET 6 BA 6 GLY B 246 HIS B 250 -1 O GLY B 246 N VAL B 258 SHEET 1 BB 3 ARG B 264 SER B 265 0 SHEET 2 BB 3 ILE B 312 ASP B 315 -1 O VAL B 314 N ARG B 264 SHEET 3 BB 3 ASP B 318 LEU B 324 -1 N ASP B 318 O ASP B 315 SHEET 1 BC 2 TYR B 302 VAL B 303 0 SHEET 2 BC 2 PHE B 331 ARG B 332 -1 O PHE B 331 N VAL B 303 SHEET 1 BD 2 PHE B 414 VAL B 415 0 SHEET 2 BD 2 TRP B 421 ILE B 422 -1 O ILE B 422 N PHE B 414 CISPEP 1 LEU A 394 PRO A 395 0 10.54 CISPEP 2 LEU B 394 PRO B 395 0 4.52 SITE 1 AC1 5 LYS A 430 MET A 448 LEU A 449 ASN A 452 SITE 2 AC1 5 HOH A2213 SITE 1 AC2 7 PRO A 411 GLY A 412 PRO A 413 PRO A 424 SITE 2 AC2 7 GLN A 429 LEU A 432 HOH A2224 SITE 1 AC3 6 PRO A 153 THR A 154 GLY A 155 ALA A 437 SITE 2 AC3 6 LEU A 438 HOH A2040 SITE 1 AC4 8 PRO A 237 HOH A2055 ASP B 160 LYS B 161 SITE 2 AC4 8 SER B 162 GLY B 246 PHE B 247 HOH B2014 SITE 1 AC5 7 THR B 154 ALA B 437 LEU B 438 HOH B2203 SITE 2 AC5 7 HOH B2288 HOH B2289 HOH B2290 CRYST1 91.258 54.423 91.822 90.00 91.22 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 0.010958 0.000000 0.000233 0.00000 SCALE2 0.000000 0.018375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010893 0.00000 MTRIX1 1 -0.103680 0.016020 -0.994480 141.35913 1 MTRIX2 1 -0.008200 0.999820 0.016970 -12.82482 1 MTRIX3 1 0.994580 0.009910 -0.103530 -39.77009 1