HEADER HYDROLASE 20-MAY-04 1VKH TITLE CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM TITLE 2 SACCHAROMYCES CEREVISIAE AT 1.85 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SERINE HYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: YDR428C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PUTATIVE SERINE HYDROLASE, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 9 09-OCT-24 1VKH 1 REMARK REVDAT 8 25-JAN-23 1VKH 1 REMARK SEQADV LINK REVDAT 7 13-JUL-11 1VKH 1 VERSN REVDAT 6 28-JUL-10 1VKH 1 HEADER TITLE KEYWDS REVDAT 5 24-FEB-09 1VKH 1 VERSN REVDAT 4 20-SEP-05 1VKH 1 JRNL REVDAT 3 01-FEB-05 1VKH 1 JRNL REVDAT 2 18-JAN-05 1VKH 1 AUTHOR KEYWDS REMARK REVDAT 1 08-JUN-04 1VKH 0 JRNL AUTH J.W.ARNDT,R.SCHWARZENBACHER,R.PAGE,P.ABDUBEK,E.AMBING, JRNL AUTH 2 T.BIORAC,J.M.CANAVES,H.J.CHIU,X.DAI,A.M.DEACON,M.DIDONATO, JRNL AUTH 3 M.A.ELSLIGER,A.GODZIK,C.GRITTINI,S.K.GRZECHNIK,J.HALE, JRNL AUTH 4 E.HAMPTON,G.W.HAN,J.HAUGEN,M.HORNSBY,H.E.KLOCK,E.KOESEMA, JRNL AUTH 5 A.KREUSCH,P.KUHN,L.JAROSZEWSKI,S.A.LESLEY,I.LEVIN, JRNL AUTH 6 D.MCMULLAN,T.M.MCPHILLIPS,M.D.MILLER,A.MORSE,K.MOY, JRNL AUTH 7 E.NIGOGHOSSIAN,J.OUYANG,W.S.PETI,K.QUIJANO,R.REYES,E.SIMS, JRNL AUTH 8 G.SPRAGGON,R.C.STEVENS,H.VAN DEN BEDEM,J.VELASQUEZ, JRNL AUTH 9 J.VINCENT,F.VON DELFT,X.WANG,B.WEST,A.WHITE,G.WOLF,Q.XU, JRNL AUTH10 O.ZAGNITKO,K.O.HODGSON,J.WOOLEY,I.A.WILSON JRNL TITL CRYSTAL STRUCTURE OF AN ALPHA/BETA SERINE HYDROLASE JRNL TITL 2 (YDR428C) FROM SACCHAROMYCES CEREVISIAE AT 1.85 A RESOLUTION JRNL REF PROTEINS V. 58 755 2005 JRNL REFN ISSN 0887-3585 JRNL PMID 15624212 JRNL DOI 10.1002/PROT.20336 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.9999 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 39479 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2060 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2453 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1740 REMARK 3 BIN FREE R VALUE SET COUNT : 127 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4133 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 454 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 27.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.233 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4282 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3868 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5801 ; 1.698 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9055 ; 0.909 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 505 ; 5.771 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;40.422 ;25.271 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 782 ;13.328 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;16.530 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 669 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4625 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 811 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 955 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4037 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2356 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 424 ; 0.170 ; 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): 26 ; 0.245 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 71 ; 0.266 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.237 ; 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): 2801 ; 1.496 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1030 ; 0.373 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4214 ; 1.659 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1876 ; 3.072 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1587 ; 4.247 ; 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 7 A 261 REMARK 3 ORIGIN FOR THE GROUP (A): -8.6850 31.7140 73.8620 REMARK 3 T TENSOR REMARK 3 T11: -0.1074 T22: -0.2667 REMARK 3 T33: -0.2105 T12: -0.0010 REMARK 3 T13: 0.0052 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.6720 L22: 0.5367 REMARK 3 L33: 1.1790 L12: 0.1523 REMARK 3 L13: -0.0172 L23: -0.0587 REMARK 3 S TENSOR REMARK 3 S11: -0.0142 S12: -0.0893 S13: -0.0363 REMARK 3 S21: 0.0354 S22: -0.0006 S23: -0.0654 REMARK 3 S31: 0.0542 S32: -0.0167 S33: 0.0147 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 261 REMARK 3 ORIGIN FOR THE GROUP (A): 5.0750 37.6100 41.8350 REMARK 3 T TENSOR REMARK 3 T11: -0.1262 T22: -0.2414 REMARK 3 T33: -0.2004 T12: -0.0111 REMARK 3 T13: 0.0130 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.9365 L22: 0.8011 REMARK 3 L33: 1.7341 L12: 0.0487 REMARK 3 L13: 0.0372 L23: 0.1341 REMARK 3 S TENSOR REMARK 3 S11: 0.0503 S12: 0.1310 S13: -0.0146 REMARK 3 S21: -0.0491 S22: 0.0193 S23: -0.0483 REMARK 3 S31: -0.0038 S32: -0.0144 S33: -0.0696 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS 2. NON-ROTOMERS: LEU 156 AND LEU 160 (MOLECULE REMARK 3 A AND B). REMARK 4 REMARK 4 1VKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000001951. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 8-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9464, 0.979326, 0.979179 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42225 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.890 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 17.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.57 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34300 REMARK 200 FOR SHELL : 3.570 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 (%): 35.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16.00% PEG MME 2000, 0.10M HEPES, REMARK 280 0.00M HEPES_NA, 5% GLYCEROL , VAPOR DIFFUSION,SITTING DROP, REMARK 280 NANODROP, 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 42.97950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -9.45540 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 69.84186 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 SER A 2 REMARK 465 ASN A 3 REMARK 465 MET B -11 REMARK 465 GLY B -10 REMARK 465 SER B -9 REMARK 465 ASP B -8 REMARK 465 LYS B -7 REMARK 465 ILE B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MSE B 1 REMARK 465 SER B 2 REMARK 465 ASN B 3 REMARK 465 THR B 4 REMARK 465 VAL B 5 REMARK 465 ARG B 6 REMARK 465 ALA B 7 REMARK 465 ILE B 8 REMARK 465 SER B 9 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 ARG A 6 CB CG CD NE CZ NH1 NH2 REMARK 470 GLN A 26 CG CD OE1 NE2 REMARK 470 ARG A 29 NE CZ NH1 NH2 REMARK 470 ARG B 29 NE CZ NH1 NH2 REMARK 470 GLU B 78 CG CD OE1 OE2 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 ARG A 171 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP B 151 CB - CG - OD2 ANGL. DEV. = 5.7 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 LEU A 14 32.05 75.69 REMARK 500 ASN A 41 -23.09 -142.86 REMARK 500 SER A 110 -130.28 63.06 REMARK 500 TRP B 40 -16.50 77.30 REMARK 500 SER B 110 -125.11 54.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 455 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 456 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 457 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 354901 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CLONING ARTIFACT. THE CONSTRUCT WAS PCR AMPLIFIED WITH REMARK 999 TAQ POLYMERASE. SEQUENCING OF THE CLONED CONSTRUCT REMARK 999 INDICATED THAT VAL IN POSITION 161 WAS MUTATED TO ILE. DBREF 1VKH A 1 261 UNP Q04066 Q04066_YEAST 1 261 DBREF 1VKH B 1 261 UNP Q04066 Q04066_YEAST 1 261 SEQADV 1VKH MET A -11 UNP Q04066 EXPRESSION TAG SEQADV 1VKH GLY A -10 UNP Q04066 EXPRESSION TAG SEQADV 1VKH SER A -9 UNP Q04066 EXPRESSION TAG SEQADV 1VKH ASP A -8 UNP Q04066 EXPRESSION TAG SEQADV 1VKH LYS A -7 UNP Q04066 EXPRESSION TAG SEQADV 1VKH ILE A -6 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS A -5 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS A -4 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS A -3 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS A -2 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS A -1 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS A 0 UNP Q04066 EXPRESSION TAG SEQADV 1VKH MSE A 1 UNP Q04066 MET 1 MODIFIED RESIDUE SEQADV 1VKH MSE A 60 UNP Q04066 MET 60 MODIFIED RESIDUE SEQADV 1VKH MSE A 106 UNP Q04066 MET 106 MODIFIED RESIDUE SEQADV 1VKH MSE A 130 UNP Q04066 MET 130 MODIFIED RESIDUE SEQADV 1VKH MSE A 137 UNP Q04066 MET 137 MODIFIED RESIDUE SEQADV 1VKH ILE A 161 UNP Q04066 VAL 161 SEE REMARK 999 SEQADV 1VKH MSE A 180 UNP Q04066 MET 180 MODIFIED RESIDUE SEQADV 1VKH MSE A 189 UNP Q04066 MET 189 MODIFIED RESIDUE SEQADV 1VKH MSE A 203 UNP Q04066 MET 203 MODIFIED RESIDUE SEQADV 1VKH MET B -11 UNP Q04066 EXPRESSION TAG SEQADV 1VKH GLY B -10 UNP Q04066 EXPRESSION TAG SEQADV 1VKH SER B -9 UNP Q04066 EXPRESSION TAG SEQADV 1VKH ASP B -8 UNP Q04066 EXPRESSION TAG SEQADV 1VKH LYS B -7 UNP Q04066 EXPRESSION TAG SEQADV 1VKH ILE B -6 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS B -5 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS B -4 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS B -3 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS B -2 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS B -1 UNP Q04066 EXPRESSION TAG SEQADV 1VKH HIS B 0 UNP Q04066 EXPRESSION TAG SEQADV 1VKH MSE B 1 UNP Q04066 MET 1 MODIFIED RESIDUE SEQADV 1VKH MSE B 60 UNP Q04066 MET 60 MODIFIED RESIDUE SEQADV 1VKH MSE B 106 UNP Q04066 MET 106 MODIFIED RESIDUE SEQADV 1VKH MSE B 130 UNP Q04066 MET 130 MODIFIED RESIDUE SEQADV 1VKH MSE B 137 UNP Q04066 MET 137 MODIFIED RESIDUE SEQADV 1VKH ILE B 161 UNP Q04066 VAL 161 SEE REMARK 999 SEQADV 1VKH MSE B 180 UNP Q04066 MET 180 MODIFIED RESIDUE SEQADV 1VKH MSE B 189 UNP Q04066 MET 189 MODIFIED RESIDUE SEQADV 1VKH MSE B 203 UNP Q04066 MET 203 MODIFIED RESIDUE SEQRES 1 A 273 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 273 SER ASN THR VAL ARG ALA ILE SER PRO ASP ILE THR LEU SEQRES 3 A 273 PHE ASN LYS THR LEU THR PHE GLN GLU ILE SER GLN ASN SEQRES 4 A 273 THR ARG GLU ALA VAL ILE TYR ILE HIS GLY GLY ALA TRP SEQRES 5 A 273 ASN ASP PRO GLU ASN THR PRO ASN ASP PHE ASN GLN LEU SEQRES 6 A 273 ALA ASN THR ILE LYS SER MSE ASP THR GLU SER THR VAL SEQRES 7 A 273 CYS GLN TYR SER ILE GLU TYR ARG LEU SER PRO GLU ILE SEQRES 8 A 273 THR ASN PRO ARG ASN LEU TYR ASP ALA VAL SER ASN ILE SEQRES 9 A 273 THR ARG LEU VAL LYS GLU LYS GLY LEU THR ASN ILE ASN SEQRES 10 A 273 MSE VAL GLY HIS SER VAL GLY ALA THR PHE ILE TRP GLN SEQRES 11 A 273 ILE LEU ALA ALA LEU LYS ASP PRO GLN GLU LYS MSE SER SEQRES 12 A 273 GLU ALA GLN LEU GLN MSE LEU GLY LEU LEU GLN ILE VAL SEQRES 13 A 273 LYS ARG VAL PHE LEU LEU ASP GLY ILE TYR SER LEU LYS SEQRES 14 A 273 GLU LEU LEU ILE GLU TYR PRO GLU TYR ASP CYS PHE THR SEQRES 15 A 273 ARG LEU ALA PHE PRO ASP GLY ILE GLN MSE TYR GLU GLU SEQRES 16 A 273 GLU PRO SER ARG VAL MSE PRO TYR VAL LYS LYS ALA LEU SEQRES 17 A 273 SER ARG PHE SER ILE ASP MSE HIS LEU VAL HIS SER TYR SEQRES 18 A 273 SER ASP GLU LEU LEU THR LEU ARG GLN THR ASN CYS LEU SEQRES 19 A 273 ILE SER CYS LEU GLN ASP TYR GLN LEU SER PHE LYS LEU SEQRES 20 A 273 TYR LEU ASP ASP LEU GLY LEU HIS ASN ASP VAL TYR LYS SEQRES 21 A 273 ASN GLY LYS VAL ALA LYS TYR ILE PHE ASP ASN ILE CYS SEQRES 1 B 273 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 B 273 SER ASN THR VAL ARG ALA ILE SER PRO ASP ILE THR LEU SEQRES 3 B 273 PHE ASN LYS THR LEU THR PHE GLN GLU ILE SER GLN ASN SEQRES 4 B 273 THR ARG GLU ALA VAL ILE TYR ILE HIS GLY GLY ALA TRP SEQRES 5 B 273 ASN ASP PRO GLU ASN THR PRO ASN ASP PHE ASN GLN LEU SEQRES 6 B 273 ALA ASN THR ILE LYS SER MSE ASP THR GLU SER THR VAL SEQRES 7 B 273 CYS GLN TYR SER ILE GLU TYR ARG LEU SER PRO GLU ILE SEQRES 8 B 273 THR ASN PRO ARG ASN LEU TYR ASP ALA VAL SER ASN ILE SEQRES 9 B 273 THR ARG LEU VAL LYS GLU LYS GLY LEU THR ASN ILE ASN SEQRES 10 B 273 MSE VAL GLY HIS SER VAL GLY ALA THR PHE ILE TRP GLN SEQRES 11 B 273 ILE LEU ALA ALA LEU LYS ASP PRO GLN GLU LYS MSE SER SEQRES 12 B 273 GLU ALA GLN LEU GLN MSE LEU GLY LEU LEU GLN ILE VAL SEQRES 13 B 273 LYS ARG VAL PHE LEU LEU ASP GLY ILE TYR SER LEU LYS SEQRES 14 B 273 GLU LEU LEU ILE GLU TYR PRO GLU TYR ASP CYS PHE THR SEQRES 15 B 273 ARG LEU ALA PHE PRO ASP GLY ILE GLN MSE TYR GLU GLU SEQRES 16 B 273 GLU PRO SER ARG VAL MSE PRO TYR VAL LYS LYS ALA LEU SEQRES 17 B 273 SER ARG PHE SER ILE ASP MSE HIS LEU VAL HIS SER TYR SEQRES 18 B 273 SER ASP GLU LEU LEU THR LEU ARG GLN THR ASN CYS LEU SEQRES 19 B 273 ILE SER CYS LEU GLN ASP TYR GLN LEU SER PHE LYS LEU SEQRES 20 B 273 TYR LEU ASP ASP LEU GLY LEU HIS ASN ASP VAL TYR LYS SEQRES 21 B 273 ASN GLY LYS VAL ALA LYS TYR ILE PHE ASP ASN ILE CYS MODRES 1VKH MSE A 1 MET SELENOMETHIONINE MODRES 1VKH MSE A 60 MET SELENOMETHIONINE MODRES 1VKH MSE A 106 MET SELENOMETHIONINE MODRES 1VKH MSE A 130 MET SELENOMETHIONINE MODRES 1VKH MSE A 137 MET SELENOMETHIONINE MODRES 1VKH MSE A 180 MET SELENOMETHIONINE MODRES 1VKH MSE A 189 MET SELENOMETHIONINE MODRES 1VKH MSE A 203 MET SELENOMETHIONINE MODRES 1VKH MSE B 60 MET SELENOMETHIONINE MODRES 1VKH MSE B 106 MET SELENOMETHIONINE MODRES 1VKH MSE B 130 MET SELENOMETHIONINE MODRES 1VKH MSE B 137 MET SELENOMETHIONINE MODRES 1VKH MSE B 180 MET SELENOMETHIONINE MODRES 1VKH MSE B 189 MET SELENOMETHIONINE MODRES 1VKH MSE B 203 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 60 8 HET MSE A 106 12 HET MSE A 130 8 HET MSE A 137 8 HET MSE A 180 8 HET MSE A 189 8 HET MSE A 203 8 HET MSE B 60 8 HET MSE B 106 12 HET MSE B 130 8 HET MSE B 137 8 HET MSE B 180 8 HET MSE B 189 8 HET MSE B 203 12 HET GOL A 456 6 HET GOL A 457 6 HET CL B 455 2 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 15(C5 H11 N O2 SE) FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 CL CL 1- FORMUL 6 HOH *454(H2 O) HELIX 1 1 LEU A 14 THR A 18 5 5 HELIX 2 2 THR A 46 ASP A 49 5 4 HELIX 3 3 PHE A 50 ASP A 61 1 12 HELIX 4 4 PRO A 82 GLY A 100 1 19 HELIX 5 5 SER A 110 ALA A 121 1 12 HELIX 6 6 ALA A 122 ASP A 125 5 4 HELIX 7 7 SER A 131 GLN A 142 1 12 HELIX 8 8 SER A 155 TYR A 163 1 9 HELIX 9 9 TYR A 166 PHE A 174 1 9 HELIX 10 10 GLY A 177 TYR A 181 5 5 HELIX 11 11 GLU A 184 SER A 200 1 17 HELIX 12 12 LEU A 216 TYR A 229 1 14 HELIX 13 13 LEU A 242 LYS A 248 5 7 HELIX 14 14 ASN A 249 ASN A 259 1 11 HELIX 15 15 LEU B 14 THR B 18 5 5 HELIX 16 16 THR B 46 ASP B 49 5 4 HELIX 17 17 PHE B 50 ASP B 61 1 12 HELIX 18 18 PRO B 82 GLY B 100 1 19 HELIX 19 19 SER B 110 ALA B 121 1 12 HELIX 20 20 ALA B 122 ASP B 125 5 4 HELIX 21 21 SER B 131 GLN B 142 1 12 HELIX 22 22 SER B 155 TYR B 163 1 9 HELIX 23 23 TYR B 166 PHE B 174 1 9 HELIX 24 24 GLY B 177 TYR B 181 5 5 HELIX 25 25 GLU B 184 SER B 200 1 17 HELIX 26 26 LEU B 216 TYR B 229 1 14 HELIX 27 27 LEU B 242 LYS B 248 5 7 HELIX 28 28 ASN B 249 ASN B 259 1 11 SHEET 1 A14 LEU A 19 GLN A 22 0 SHEET 2 A14 VAL A 66 ILE A 71 -1 O GLN A 68 N GLN A 22 SHEET 3 A14 GLU A 30 ILE A 35 1 N TYR A 34 O TYR A 69 SHEET 4 A14 ILE A 104 HIS A 109 1 O VAL A 107 N ILE A 33 SHEET 5 A14 VAL A 144 LEU A 150 1 O LYS A 145 N ILE A 104 SHEET 6 A14 ASP A 202 SER A 208 1 O HIS A 204 N LEU A 149 SHEET 7 A14 PHE A 233 ASP A 238 1 O LYS A 234 N LEU A 205 SHEET 8 A14 PHE B 233 ASP B 238 -1 O PHE B 233 N LEU A 237 SHEET 9 A14 ASP B 202 SER B 208 1 N LEU B 205 O LYS B 234 SHEET 10 A14 VAL B 144 LEU B 150 1 N LEU B 149 O HIS B 204 SHEET 11 A14 ILE B 104 HIS B 109 1 N GLY B 108 O LEU B 150 SHEET 12 A14 GLU B 30 ILE B 35 1 N ILE B 33 O ASN B 105 SHEET 13 A14 VAL B 66 ILE B 71 1 O TYR B 69 N TYR B 34 SHEET 14 A14 LEU B 19 GLN B 22 -1 N LEU B 19 O SER B 70 LINK C HIS A 0 N MSE A 1 1555 1555 1.34 LINK C SER A 59 N MSE A 60 1555 1555 1.33 LINK C MSE A 60 N ASP A 61 1555 1555 1.34 LINK C ASN A 105 N MSE A 106 1555 1555 1.33 LINK C MSE A 106 N VAL A 107 1555 1555 1.33 LINK C LYS A 129 N MSE A 130 1555 1555 1.33 LINK C MSE A 130 N SER A 131 1555 1555 1.33 LINK C GLN A 136 N MSE A 137 1555 1555 1.34 LINK C MSE A 137 N LEU A 138 1555 1555 1.34 LINK C GLN A 179 N MSE A 180 1555 1555 1.34 LINK C MSE A 180 N TYR A 181 1555 1555 1.33 LINK C VAL A 188 N MSE A 189 1555 1555 1.32 LINK C MSE A 189 N PRO A 190 1555 1555 1.32 LINK C ASP A 202 N MSE A 203 1555 1555 1.34 LINK C MSE A 203 N HIS A 204 1555 1555 1.33 LINK C SER B 59 N MSE B 60 1555 1555 1.33 LINK C MSE B 60 N ASP B 61 1555 1555 1.34 LINK C ASN B 105 N MSE B 106 1555 1555 1.34 LINK C MSE B 106 N VAL B 107 1555 1555 1.33 LINK C LYS B 129 N MSE B 130 1555 1555 1.32 LINK C MSE B 130 N SER B 131 1555 1555 1.34 LINK C GLN B 136 N MSE B 137 1555 1555 1.32 LINK C MSE B 137 N LEU B 138 1555 1555 1.33 LINK C GLN B 179 N MSE B 180 1555 1555 1.33 LINK C MSE B 180 N TYR B 181 1555 1555 1.33 LINK C VAL B 188 N MSE B 189 1555 1555 1.32 LINK C MSE B 189 N PRO B 190 1555 1555 1.33 LINK C ASP B 202 N MSE B 203 1555 1555 1.33 LINK C MSE B 203 N HIS B 204 1555 1555 1.33 CISPEP 1 SER A 9 PRO A 10 0 -11.49 CISPEP 2 SER A 76 PRO A 77 0 7.00 CISPEP 3 ASN A 81 PRO A 82 0 1.42 CISPEP 4 SER B 76 PRO B 77 0 13.13 CISPEP 5 ASN B 81 PRO B 82 0 5.17 SITE 1 AC1 7 SER A 131 GLU A 132 ALA A 133 SER B 131 SITE 2 AC1 7 GLU B 132 ALA B 133 HOH B 547 SITE 1 AC2 6 THR A 28 ARG A 29 GLU A 30 GLY A 100 SITE 2 AC2 6 THR A 102 ASN A 103 SITE 1 AC3 2 ASP A 228 HOH A 673 CRYST1 41.967 85.959 70.479 90.00 97.71 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 0.023828 0.000000 0.003226 0.00000 SCALE2 0.000000 0.011633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014318 0.00000