PDB Short entry for 1ZTD HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 26-MAY-05 1ZTD TITLE HYPOTHETICAL PROTEIN PFU-631545-001 FROM PYROCOCCUS FURIOSUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN PFU-631545-001; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: C41 PRIL; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24D BAM KEYWDS STRUCTURAL GENOMICS, SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS, KEYWDS 2 SECSG, PROTEIN STRUCTURE INITIATIVE, PSI, CONSERVED HYPOTHETICAL KEYWDS 3 PROTEIN, PYROCOCCUS FURIOSUS, HYPERTHERMOPHILE, PFU-631545-001, KEYWDS 4 UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Z.-Q.FU,P.HORANYI,Q.FLORENCE,Z.-J.LIU,L.CHEN,D.LEE,J.HABEL,H.XU, AUTHOR 2 D.NGUYEN,S.-H.CHANG,W.ZHOU,H.ZHANG,F.E.JENNEY JR.,B.SHA,M.W.W.ADAMS, AUTHOR 3 J.P.ROSE,B.-C.WANG,SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS AUTHOR 4 (SECSG) REVDAT 4 14-FEB-24 1ZTD 1 REMARK REVDAT 3 11-OCT-17 1ZTD 1 REMARK REVDAT 2 24-FEB-09 1ZTD 1 VERSN REVDAT 1 07-JUN-05 1ZTD 0 JRNL AUTH Z.-Q.FU,P.HORANYI,Q.FLORENCE,Z.-J.LIU,L.CHEN,D.LEE,J.HABEL, JRNL AUTH 2 H.XU,D.NGUYEN,S.-H.CHANG,W.ZHOU,H.ZHANG,F.E.JENNEY JR., JRNL AUTH 3 B.SHA,M.W.W.ADAMS,J.P.ROSE,B.-C.WANG JRNL TITL HYPOTHETICAL PROTEIN PFU-631545-001 FROM PYROCOCCUS FURIOSUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 260232.730 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 15008 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 SET) : 0.234 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 758 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1239 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 69 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1942 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.25000 REMARK 3 B22 (A**2) : -4.80000 REMARK 3 B33 (A**2) : 3.55100 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.04 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.630 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.460 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.400 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.570 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 63.89 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZTD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97941 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SAINT, LSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15035 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 9.920 REMARK 200 R MERGE (I) : 0.08250 REMARK 200 R SYM (I) : 0.08250 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.7200 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.22900 REMARK 200 R SYM FOR SHELL (I) : 0.22900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.070 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SGXPRO, SHELXD, SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% W/V PEG-8000, PH 8.2, SITTING DROP, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 291K, PH 8.20 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 30.54650 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 ALA A -7 REMARK 465 HIS 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 GLY A 0 REMARK 465 ALA B -7 REMARK 465 HIS 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 GLY B 0 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 ASP A 33 119.36 -162.00 REMARK 500 SER B 50 0.54 -66.26 REMARK 500 LEU B 53 -177.20 -60.65 REMARK 500 SER B 123 -72.18 -128.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: PFU-631545-001 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CURRENTLY THERE IS NO PROTEIN SEQUENCE DATABASE REFERENCE REMARK 999 AVAILABLE FOR THIS ENTRY. DBREF 1ZTD A 2 125 UNP Q8U363 Q8U363_PYRFU 2 125 DBREF 1ZTD B 2 125 UNP Q8U363 Q8U363_PYRFU 2 125 SEQRES 1 A 133 ALA HIS HIS HIS HIS HIS HIS GLY SER GLU ILE ASP LYS SEQRES 2 A 133 GLY LEU ALA LYS PHE GLY ASP SER LEU ILE ASN PHE LEU SEQRES 3 A 133 TYR SER LEU ALA LEU THR GLU PHE LEU GLY LYS PRO THR SEQRES 4 A 133 GLY ASP ARG VAL PRO ASN ALA SER LEU ALA ILE ALA LEU SEQRES 5 A 133 GLU LEU THR GLY LEU SER LYS ASN LEU ARG ARG VAL ASP SEQRES 6 A 133 LYS HIS ALA LYS GLY ASP TYR ALA GLU ALA LEU ILE ALA SEQRES 7 A 133 LYS ALA TRP LEU MET GLY LEU ILE SER GLU ARG GLU ALA SEQRES 8 A 133 VAL GLU ILE ILE LYS LYS ASN LEU TYR PRO GLU VAL LEU SEQRES 9 A 133 ASP PHE SER LYS LYS LYS GLU ALA ILE GLY ARG ALA LEU SEQRES 10 A 133 ALA PRO LEU LEU VAL ILE ILE SER GLU ARG LEU TYR SER SEQRES 11 A 133 SER GLN VAL SEQRES 1 B 133 ALA HIS HIS HIS HIS HIS HIS GLY SER GLU ILE ASP LYS SEQRES 2 B 133 GLY LEU ALA LYS PHE GLY ASP SER LEU ILE ASN PHE LEU SEQRES 3 B 133 TYR SER LEU ALA LEU THR GLU PHE LEU GLY LYS PRO THR SEQRES 4 B 133 GLY ASP ARG VAL PRO ASN ALA SER LEU ALA ILE ALA LEU SEQRES 5 B 133 GLU LEU THR GLY LEU SER LYS ASN LEU ARG ARG VAL ASP SEQRES 6 B 133 LYS HIS ALA LYS GLY ASP TYR ALA GLU ALA LEU ILE ALA SEQRES 7 B 133 LYS ALA TRP LEU MET GLY LEU ILE SER GLU ARG GLU ALA SEQRES 8 B 133 VAL GLU ILE ILE LYS LYS ASN LEU TYR PRO GLU VAL LEU SEQRES 9 B 133 ASP PHE SER LYS LYS LYS GLU ALA ILE GLY ARG ALA LEU SEQRES 10 B 133 ALA PRO LEU LEU VAL ILE ILE SER GLU ARG LEU TYR SER SEQRES 11 B 133 SER GLN VAL FORMUL 3 HOH *63(H2 O) HELIX 1 1 ASP A 4 GLY A 28 1 25 HELIX 2 2 PRO A 36 THR A 47 1 12 HELIX 3 3 GLY A 48 LEU A 53 5 6 HELIX 4 4 ARG A 54 LYS A 58 5 5 HELIX 5 5 ALA A 60 MET A 75 1 16 HELIX 6 6 SER A 79 LYS A 89 1 11 HELIX 7 7 ASN A 90 LEU A 91 5 2 HELIX 8 8 TYR A 92 ASP A 97 5 6 HELIX 9 9 LYS A 100 SER A 122 1 23 HELIX 10 10 ASP B 4 GLY B 28 1 25 HELIX 11 11 PRO B 36 THR B 47 1 12 HELIX 12 12 GLY B 48 ASN B 52 5 5 HELIX 13 13 ARG B 55 HIS B 59 5 5 HELIX 14 14 ALA B 60 MET B 75 1 16 HELIX 15 15 SER B 79 ASN B 90 1 12 HELIX 16 16 LEU B 91 ASP B 97 5 7 HELIX 17 17 LYS B 100 SER B 122 1 23 CRYST1 36.352 61.093 51.582 90.00 97.62 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 0.027509 0.000000 0.003680 0.00000 SCALE2 0.000000 0.016368 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019559 0.00000