PDB Short entry for 1VK3 HEADER LIGASE 23-APR-04 1VK3 TITLE CRYSTAL STRUCTURE OF PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE II TITLE 2 (TM1246) FROM THERMOTOGA MARITIMA AT 2.15 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE II; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FGAM SYNTHASE II; COMPND 5 EC: 6.3.5.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: PURL, TM1246; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TM1246, PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE II, STRUCTURAL KEYWDS 2 GENOMICS, JCSG, PSI, PROTEIN STRUCTURE INITIATIVE, JOINT CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 25-JAN-23 1VK3 1 SEQADV LINK REVDAT 5 24-FEB-09 1VK3 1 VERSN REVDAT 4 03-OCT-06 1VK3 1 JRNL REVDAT 3 28-MAR-06 1VK3 1 JRNL REVDAT 2 18-JAN-05 1VK3 1 AUTHOR KEYWDS REMARK REVDAT 1 11-MAY-04 1VK3 0 JRNL AUTH I.I.MATHEWS,S.S.KRISHNA,R.SCHWARZENBACHER,D.MCMULLAN, JRNL AUTH 2 P.ABDUBEK,E.AMBING,J.M.CANAVES,H.J.CHIU,A.M.DEACON, JRNL AUTH 3 M.DIDONATO,M.A.ELSLIGER,A.GODZIK,C.GRITTINI,S.K.GRZECHNIK, JRNL AUTH 4 J.HALE,E.HAMPTON,G.W.HAN,J.HAUGEN,L.JAROSZEWSKI,H.E.KLOCK, JRNL AUTH 5 E.KOESEMA,A.KREUSCH,P.KUHN,S.A.LESLEY,I.LEVIN,M.D.MILLER, JRNL AUTH 6 K.MOY,E.NIGOGHOSSIAN,J.PAULSEN,K.QUIJANO,R.REYES,G.SPRAGGON, JRNL AUTH 7 R.C.STEVENS,H.VAN DEN BEDEM,J.VELASQUEZ,A.WHITE,G.WOLF,Q.XU, JRNL AUTH 8 K.O.HODGSON,J.WOOLEY,I.A.WILSON JRNL TITL CRYSTAL STRUCTURE OF PHOSPHORIBOSYLFORMYLGLYCINAMIDINE JRNL TITL 2 SYNTHASE II (SMPURL) FROM THERMOTOGA MARITIMA AT 2.15 A JRNL TITL 3 RESOLUTION. JRNL REF PROTEINS V. 63 1106 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 16544324 JRNL DOI 10.1002/PROT.20650 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0001 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 26869 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1368 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1225 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4441 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -1.52000 REMARK 3 B33 (A**2) : 1.66000 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): 0.318 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.239 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.207 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4535 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6164 ; 1.315 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 6.044 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;37.563 ;23.966 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 751 ;16.934 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;17.362 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 712 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3402 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2070 ; 0.201 ; 0.200 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): 263 ; 0.144 ; 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): 50 ; 0.204 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.194 ; 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): 2988 ; 1.758 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4700 ; 2.597 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1736 ; 5.423 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1464 ; 7.269 ;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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 34 REMARK 3 RESIDUE RANGE : A 163 A 341 REMARK 3 ORIGIN FOR THE GROUP (A): 18.7890 42.2160 36.2260 REMARK 3 T TENSOR REMARK 3 T11: 0.0030 T22: 0.0260 REMARK 3 T33: -0.0341 T12: 0.0138 REMARK 3 T13: 0.0120 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 1.0952 L22: 1.2122 REMARK 3 L33: 1.5736 L12: -0.0716 REMARK 3 L13: 1.0228 L23: -0.0508 REMARK 3 S TENSOR REMARK 3 S11: -0.0203 S12: -0.0192 S13: -0.0819 REMARK 3 S21: -0.0051 S22: 0.0360 S23: -0.0237 REMARK 3 S31: 0.1253 S32: -0.0415 S33: -0.0157 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 35 A 162 REMARK 3 RESIDUE RANGE : A 342 A 506 REMARK 3 ORIGIN FOR THE GROUP (A): 17.0320 64.6740 51.6160 REMARK 3 T TENSOR REMARK 3 T11: 0.0113 T22: 0.0311 REMARK 3 T33: -0.0159 T12: 0.0029 REMARK 3 T13: 0.0264 T23: -0.0236 REMARK 3 L TENSOR REMARK 3 L11: 0.7048 L22: 0.8631 REMARK 3 L33: 0.6876 L12: 0.0230 REMARK 3 L13: 0.3500 L23: -0.1218 REMARK 3 S TENSOR REMARK 3 S11: 0.0237 S12: -0.0133 S13: 0.0237 REMARK 3 S21: 0.0082 S22: -0.0303 S23: 0.0565 REMARK 3 S31: 0.0294 S32: -0.0044 S33: 0.0067 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 : A 507 A 603 REMARK 3 ORIGIN FOR THE GROUP (A): 23.1870 83.0430 65.3200 REMARK 3 T TENSOR REMARK 3 T11: -0.0558 T22: -0.0266 REMARK 3 T33: -0.0340 T12: -0.0075 REMARK 3 T13: -0.0145 T23: -0.0651 REMARK 3 L TENSOR REMARK 3 L11: 2.1202 L22: 2.7010 REMARK 3 L33: 2.9703 L12: 0.0838 REMARK 3 L13: 0.0000 L23: -0.6145 REMARK 3 S TENSOR REMARK 3 S11: -0.0633 S12: -0.1705 S13: 0.1342 REMARK 3 S21: 0.0922 S22: -0.0477 S23: -0.0106 REMARK 3 S31: -0.1811 S32: 0.0581 S33: 0.1110 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: NULL REMARK 4 REMARK 4 1VK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000001938. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0035, 0.9796 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 4.2), CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28272 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 72.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.55400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30.00% PEG 200, 0.10M TRIS PH 8.0, 7% REMARK 280 NP_PEG 4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.88750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.20900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.34450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.20900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.88750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.34450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MSE A 1 REMARK 465 ILE A 187 REMARK 465 HIS A 188 REMARK 465 GLY A 189 REMARK 465 ALA A 190 REMARK 465 SER A 191 REMARK 465 PHE A 192 REMARK 465 ALA A 193 REMARK 465 SER A 194 REMARK 465 GLU A 195 REMARK 465 ASP A 196 REMARK 465 LEU A 197 REMARK 465 THR A 198 REMARK 465 GLY A 199 REMARK 465 ASP A 200 REMARK 465 LYS A 201 REMARK 465 ALA A 202 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 2 CG CD CE NZ REMARK 470 GLU A 11 CG CD OE1 OE2 REMARK 470 ASN A 53 CG OD1 ND2 REMARK 470 ARG A 159 NE CZ NH1 NH2 REMARK 470 ILE A 207 CB CG1 CG2 CD1 REMARK 470 GLU A 227 CG CD OE1 OE2 REMARK 470 GLU A 313 CD OE1 OE2 REMARK 470 ARG A 358 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 360 CG CD OE1 OE2 REMARK 470 GLU A 362 CD OE1 OE2 REMARK 470 ARG A 367 CZ NH1 NH2 REMARK 470 GLN A 372 CG CD OE1 NE2 REMARK 470 LYS A 395 CD CE NZ REMARK 470 GLN A 486 CG CD OE1 NE2 REMARK 470 ARG A 554 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 558 CD OE1 OE2 REMARK 470 LYS A 566 CG CD CE NZ REMARK 470 GLU A 568 CG CD OE1 OE2 REMARK 470 LYS A 570 CE NZ REMARK 470 GLU A 586 CD OE1 OE2 REMARK 470 ARG A 603 CD NE CZ NH1 NH2 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 107 CB - CG - OD2 ANGL. DEV. = 5.4 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 PHE A 50 -26.88 87.71 REMARK 500 ASP A 61 -24.87 81.92 REMARK 500 HIS A 72 41.47 -141.06 REMARK 500 MSE A 162 31.12 -146.68 REMARK 500 ASP A 262 -1.27 -59.23 REMARK 500 ASP A 270 35.69 -91.15 REMARK 500 LEU A 305 30.32 71.83 REMARK 500 ARG A 325 -117.72 52.64 REMARK 500 GLU A 360 93.80 -64.72 REMARK 500 ASP A 380 55.17 -97.94 REMARK 500 LEU A 551 -65.11 69.75 REMARK 500 ASP A 592 34.78 -86.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 283111 RELATED DB: TARGETDB DBREF 1VK3 A 1 603 UNP Q9X0X3 PURL_THEMA 1 603 SEQADV 1VK3 MET A -11 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 GLY A -10 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 SER A -9 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 ASP A -8 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 LYS A -7 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 ILE A -6 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 HIS A -5 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 HIS A -4 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 HIS A -3 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 HIS A -2 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 HIS A -1 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 HIS A 0 UNP Q9X0X3 EXPRESSION TAG SEQADV 1VK3 MSE A 1 UNP Q9X0X3 MET 1 MODIFIED RESIDUE SEQADV 1VK3 MSE A 28 UNP Q9X0X3 MET 28 MODIFIED RESIDUE SEQADV 1VK3 MSE A 98 UNP Q9X0X3 MET 98 MODIFIED RESIDUE SEQADV 1VK3 MSE A 111 UNP Q9X0X3 MET 111 MODIFIED RESIDUE SEQADV 1VK3 MSE A 162 UNP Q9X0X3 MET 162 MODIFIED RESIDUE SEQADV 1VK3 MSE A 217 UNP Q9X0X3 MET 217 MODIFIED RESIDUE SEQADV 1VK3 MSE A 225 UNP Q9X0X3 MET 225 MODIFIED RESIDUE SEQADV 1VK3 MSE A 271 UNP Q9X0X3 MET 271 MODIFIED RESIDUE SEQADV 1VK3 MSE A 285 UNP Q9X0X3 MET 285 MODIFIED RESIDUE SEQADV 1VK3 MSE A 323 UNP Q9X0X3 MET 323 MODIFIED RESIDUE SEQADV 1VK3 MSE A 330 UNP Q9X0X3 MET 330 MODIFIED RESIDUE SEQADV 1VK3 MSE A 376 UNP Q9X0X3 MET 376 MODIFIED RESIDUE SEQADV 1VK3 MSE A 392 UNP Q9X0X3 MET 392 MODIFIED RESIDUE SEQADV 1VK3 MSE A 459 UNP Q9X0X3 MET 459 MODIFIED RESIDUE SEQADV 1VK3 MSE A 460 UNP Q9X0X3 MET 460 MODIFIED RESIDUE SEQADV 1VK3 MSE A 498 UNP Q9X0X3 MET 498 MODIFIED RESIDUE SEQADV 1VK3 MSE A 580 UNP Q9X0X3 MET 580 MODIFIED RESIDUE SEQRES 1 A 615 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 615 LYS LEU ARG TYR LEU ASN ILE LEU LYS GLU LYS LEU GLY SEQRES 3 A 615 ARG GLU PRO THR PHE VAL GLU LEU GLN ALA PHE SER VAL SEQRES 4 A 615 MSE TRP SER GLU HIS CYS GLY TYR SER HIS THR LYS LYS SEQRES 5 A 615 TYR ILE ARG ARG LEU PRO LYS THR GLY PHE GLU GLY ASN SEQRES 6 A 615 ALA GLY VAL VAL ASN LEU ASP ASP TYR TYR SER VAL ALA SEQRES 7 A 615 PHE LYS ILE GLU SER HIS ASN HIS PRO SER ALA ILE GLU SEQRES 8 A 615 PRO TYR ASN GLY ALA ALA THR GLY VAL GLY GLY ILE ILE SEQRES 9 A 615 ARG ASP VAL LEU ALA MSE GLY ALA ARG PRO THR ALA ILE SEQRES 10 A 615 PHE ASP SER LEU HIS MSE SER ARG ILE ILE ASP GLY ILE SEQRES 11 A 615 ILE GLU GLY ILE ALA ASP TYR GLY ASN SER ILE GLY VAL SEQRES 12 A 615 PRO THR VAL GLY GLY GLU LEU ARG ILE SER SER LEU TYR SEQRES 13 A 615 ALA HIS ASN PRO LEU VAL ASN VAL LEU ALA ALA GLY VAL SEQRES 14 A 615 VAL ARG ASN ASP MSE LEU VAL ASP SER LYS ALA SER ARG SEQRES 15 A 615 PRO GLY GLN VAL ILE VAL ILE PHE GLY GLY ALA THR GLY SEQRES 16 A 615 ARG ASP GLY ILE HIS GLY ALA SER PHE ALA SER GLU ASP SEQRES 17 A 615 LEU THR GLY ASP LYS ALA THR LYS LEU SER ILE GLN VAL SEQRES 18 A 615 GLY ASP PRO PHE ALA GLU LYS MSE LEU ILE GLU ALA PHE SEQRES 19 A 615 LEU GLU MSE VAL GLU GLU GLY LEU VAL GLU GLY ALA GLN SEQRES 20 A 615 ASP LEU GLY ALA GLY GLY VAL LEU SER ALA THR SER GLU SEQRES 21 A 615 LEU VAL ALA LYS GLY ASN LEU GLY ALA ILE VAL HIS LEU SEQRES 22 A 615 ASP ARG VAL PRO LEU ARG GLU PRO ASP MSE GLU PRO TRP SEQRES 23 A 615 GLU ILE LEU ILE SER GLU SER GLN GLU ARG MSE ALA VAL SEQRES 24 A 615 VAL THR SER PRO GLN LYS ALA SER ARG ILE LEU GLU ILE SEQRES 25 A 615 ALA ARG LYS HIS LEU LEU PHE GLY ASP VAL VAL ALA GLU SEQRES 26 A 615 VAL ILE GLU GLU PRO VAL TYR ARG VAL MSE TYR ARG ASN SEQRES 27 A 615 ASP LEU VAL MSE GLU VAL PRO VAL GLN LEU LEU ALA ASN SEQRES 28 A 615 ALA PRO GLU GLU ASP ILE VAL GLU TYR THR PRO GLY LYS SEQRES 29 A 615 ILE PRO GLU PHE LYS ARG VAL GLU PHE GLU GLU VAL ASN SEQRES 30 A 615 ALA ARG GLU VAL PHE GLU GLN TYR ASP HIS MSE VAL GLY SEQRES 31 A 615 THR ASP THR VAL VAL PRO PRO GLY PHE GLY ALA ALA VAL SEQRES 32 A 615 MSE ARG ILE LYS ARG ASP GLY GLY TYR SER LEU VAL THR SEQRES 33 A 615 HIS SER ARG ALA ASP LEU ALA LEU GLN ASP THR TYR TRP SEQRES 34 A 615 GLY THR LEU ILE ALA VAL LEU GLU SER VAL ARG LYS THR SEQRES 35 A 615 LEU SER VAL GLY ALA GLU PRO LEU ALA ILE THR ASN CYS SEQRES 36 A 615 VAL ASN TYR GLY ASP PRO ASP VAL ASP PRO VAL GLY LEU SEQRES 37 A 615 SER ALA MSE MSE THR ALA LEU LYS ASN ALA CYS GLU PHE SEQRES 38 A 615 SER GLY VAL PRO VAL ALA SER GLY ASN ALA SER LEU TYR SEQRES 39 A 615 ASN THR TYR GLN GLY LYS PRO ILE PRO PRO THR LEU VAL SEQRES 40 A 615 VAL GLY MSE LEU GLY LYS VAL ASN PRO GLN LYS VAL ALA SEQRES 41 A 615 LYS PRO LYS PRO SER LYS VAL PHE ALA VAL GLY TRP ASN SEQRES 42 A 615 ASP PHE GLU LEU GLU ARG GLU LYS GLU LEU TRP ARG ALA SEQRES 43 A 615 ILE ARG LYS LEU SER GLU GLU GLY ALA PHE ILE LEU SER SEQRES 44 A 615 SER SER GLN LEU LEU THR ARG THR HIS VAL GLU THR PHE SEQRES 45 A 615 ARG GLU TYR GLY LEU LYS ILE GLU VAL LYS LEU PRO GLU SEQRES 46 A 615 VAL ARG PRO ALA HIS GLN MSE VAL LEU VAL PHE SER GLU SEQRES 47 A 615 ARG THR PRO VAL VAL ASP VAL PRO VAL LYS GLU ILE GLY SEQRES 48 A 615 THR LEU SER ARG MODRES 1VK3 MSE A 28 MET SELENOMETHIONINE MODRES 1VK3 MSE A 98 MET SELENOMETHIONINE MODRES 1VK3 MSE A 111 MET SELENOMETHIONINE MODRES 1VK3 MSE A 162 MET SELENOMETHIONINE MODRES 1VK3 MSE A 217 MET SELENOMETHIONINE MODRES 1VK3 MSE A 225 MET SELENOMETHIONINE MODRES 1VK3 MSE A 271 MET SELENOMETHIONINE MODRES 1VK3 MSE A 285 MET SELENOMETHIONINE MODRES 1VK3 MSE A 323 MET SELENOMETHIONINE MODRES 1VK3 MSE A 330 MET SELENOMETHIONINE MODRES 1VK3 MSE A 376 MET SELENOMETHIONINE MODRES 1VK3 MSE A 392 MET SELENOMETHIONINE MODRES 1VK3 MSE A 459 MET SELENOMETHIONINE MODRES 1VK3 MSE A 460 MET SELENOMETHIONINE MODRES 1VK3 MSE A 498 MET SELENOMETHIONINE MODRES 1VK3 MSE A 580 MET SELENOMETHIONINE HET MSE A 28 8 HET MSE A 98 8 HET MSE A 111 8 HET MSE A 162 8 HET MSE A 217 8 HET MSE A 225 8 HET MSE A 271 8 HET MSE A 285 8 HET MSE A 323 8 HET MSE A 330 8 HET MSE A 376 8 HET MSE A 392 8 HET MSE A 459 8 HET MSE A 460 8 HET MSE A 498 8 HET MSE A 580 8 HET CL A 604 1 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION FORMUL 1 MSE 16(C5 H11 N O2 SE) FORMUL 2 CL CL 1- FORMUL 3 HOH *221(H2 O) HELIX 1 1 LYS A 2 GLY A 14 1 13 HELIX 2 2 THR A 18 TRP A 29 1 12 HELIX 3 3 SER A 30 TYR A 35 1 6 HELIX 4 4 THR A 38 ARG A 44 1 7 HELIX 5 5 ASN A 73 GLU A 79 1 7 HELIX 6 6 GLU A 79 MSE A 98 1 20 HELIX 7 7 ILE A 115 ILE A 129 1 15 HELIX 8 8 SER A 142 ALA A 145 5 4 HELIX 9 9 THR A 203 ILE A 207 5 5 HELIX 10 10 PRO A 212 GLY A 229 1 18 HELIX 11 11 GLY A 241 LYS A 252 1 12 HELIX 12 12 ASP A 262 VAL A 264 5 3 HELIX 13 13 GLU A 272 SER A 279 1 8 HELIX 14 14 SER A 290 GLN A 292 5 3 HELIX 15 15 ALA A 294 HIS A 304 1 11 HELIX 16 16 VAL A 334 ASN A 339 1 6 HELIX 17 17 ASN A 365 GLU A 371 1 7 HELIX 18 18 PRO A 384 GLY A 388 5 5 HELIX 19 19 ARG A 407 LEU A 412 1 6 HELIX 20 20 ASP A 414 SER A 432 1 19 HELIX 21 21 PRO A 453 GLY A 471 1 19 HELIX 22 22 ASN A 503 VAL A 507 5 5 HELIX 23 23 GLU A 524 GLU A 526 5 3 HELIX 24 24 ARG A 527 GLU A 541 1 15 HELIX 25 25 THR A 553 TYR A 563 1 11 SHEET 1 A 6 VAL A 56 ASN A 58 0 SHEET 2 A 6 TYR A 63 SER A 71 -1 O VAL A 65 N VAL A 57 SHEET 3 A 6 LEU A 149 ARG A 159 -1 O VAL A 158 N SER A 64 SHEET 4 A 6 ARG A 101 MSE A 111 -1 N SER A 108 O ASN A 151 SHEET 5 A 6 THR A 133 ILE A 140 1 O GLU A 137 N ASP A 107 SHEET 6 A 6 GLU A 362 GLU A 363 -1 O GLU A 362 N ILE A 140 SHEET 1 B 7 GLY A 233 ASP A 236 0 SHEET 2 B 7 ARG A 284 THR A 289 -1 O VAL A 288 N GLY A 233 SHEET 3 B 7 VAL A 174 GLY A 179 -1 N VAL A 176 O VAL A 287 SHEET 4 B 7 PHE A 307 ILE A 315 -1 O VAL A 311 N ILE A 175 SHEET 5 B 7 GLY A 256 HIS A 260 -1 N HIS A 260 O VAL A 311 SHEET 6 B 7 VAL A 319 TYR A 324 1 O MSE A 323 N VAL A 259 SHEET 7 B 7 ASP A 327 PRO A 333 -1 O VAL A 332 N TYR A 320 SHEET 1 C 5 ALA A 390 LYS A 395 0 SHEET 2 C 5 GLY A 398 HIS A 405 -1 O TYR A 400 N MSE A 392 SHEET 3 C 5 THR A 493 VAL A 502 -1 O VAL A 496 N HIS A 405 SHEET 4 C 5 GLU A 436 ASN A 445 -1 N LEU A 438 O LEU A 499 SHEET 5 C 5 VAL A 474 SER A 480 1 O SER A 480 N VAL A 444 SHEET 1 D 2 THR A 484 TYR A 485 0 SHEET 2 D 2 LYS A 488 PRO A 489 -1 O LYS A 488 N TYR A 485 SHEET 1 E 5 PHE A 544 LEU A 546 0 SHEET 2 E 5 GLN A 579 SER A 585 -1 O PHE A 584 N PHE A 544 SHEET 3 E 5 SER A 513 TRP A 520 -1 N LYS A 514 O SER A 585 SHEET 4 E 5 VAL A 595 SER A 602 -1 O LYS A 596 N ALA A 517 SHEET 5 E 5 LYS A 566 VAL A 569 -1 N LYS A 566 O SER A 602 LINK C VAL A 27 N MSE A 28 1555 1555 1.34 LINK C MSE A 28 N TRP A 29 1555 1555 1.33 LINK C ALA A 97 N MSE A 98 1555 1555 1.33 LINK C MSE A 98 N GLY A 99 1555 1555 1.33 LINK C HIS A 110 N MSE A 111 1555 1555 1.33 LINK C MSE A 111 N SER A 112 1555 1555 1.33 LINK C ASP A 161 N MSE A 162 1555 1555 1.33 LINK C MSE A 162 N LEU A 163 1555 1555 1.33 LINK C LYS A 216 N MSE A 217 1555 1555 1.33 LINK C MSE A 217 N LEU A 218 1555 1555 1.33 LINK C GLU A 224 N MSE A 225 1555 1555 1.34 LINK C MSE A 225 N VAL A 226 1555 1555 1.33 LINK C ASP A 270 N MSE A 271 1555 1555 1.33 LINK C MSE A 271 N GLU A 272 1555 1555 1.33 LINK C ARG A 284 N MSE A 285 1555 1555 1.33 LINK C MSE A 285 N ALA A 286 1555 1555 1.33 LINK C VAL A 322 N MSE A 323 1555 1555 1.33 LINK C MSE A 323 N TYR A 324 1555 1555 1.33 LINK C VAL A 329 N MSE A 330 1555 1555 1.34 LINK C MSE A 330 N GLU A 331 1555 1555 1.32 LINK C HIS A 375 N MSE A 376 1555 1555 1.33 LINK C MSE A 376 N VAL A 377 1555 1555 1.33 LINK C VAL A 391 N MSE A 392 1555 1555 1.34 LINK C MSE A 392 N ARG A 393 1555 1555 1.33 LINK C ALA A 458 N MSE A 459 1555 1555 1.33 LINK C MSE A 459 N MSE A 460 1555 1555 1.32 LINK C MSE A 460 N THR A 461 1555 1555 1.34 LINK C GLY A 497 N MSE A 498 1555 1555 1.32 LINK C MSE A 498 N LEU A 499 1555 1555 1.33 LINK C GLN A 579 N MSE A 580 1555 1555 1.33 LINK C MSE A 580 N VAL A 581 1555 1555 1.34 CRYST1 59.775 72.689 128.418 90.00 90.00 90.00 P 21 21 21 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 0.016729 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013757 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007787 0.00000