HEADER TRANSFERASE 26-FEB-99 1CBK TITLE 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE FROM HAEMOPHILUS TITLE 2 INFLUENZAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN- COMPND 3 PYROPHOSPHOKINASE); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PYROPHOSPHOKINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.HENNIG,A.D'ARCY,G.DALE,C.OEFNER REVDAT 5 27-DEC-23 1CBK 1 REMARK REVDAT 4 24-FEB-09 1CBK 1 VERSN REVDAT 3 01-APR-03 1CBK 1 JRNL REVDAT 2 17-AUG-01 1CBK 1 AUTHOR REVDAT 1 01-MAR-00 1CBK 0 JRNL AUTH M.HENNIG,G.E.DALE,A.D'ARCY,F.DANEL,S.FISCHER,C.P.GRAY, JRNL AUTH 2 S.JOLIDON,F.MULLER,M.G.PAGE,P.PATTISON,C.OEFNER JRNL TITL THE STRUCTURE AND FUNCTION OF THE JRNL TITL 2 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE FROM JRNL TITL 3 HAEMOPHILUS INFLUENZAE. JRNL REF J.MOL.BIOL. V. 287 211 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10080886 JRNL DOI 10.1006/JMBI.1999.2623 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 25768 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) : 0.162 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1288 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2580 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 404 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.722 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CBK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686,0.9796,0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25768 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 6.21000 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 16.7000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 56.38750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.39550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.38750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.39550 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 300 REMARK: THE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS ONE DIMER. 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: 3250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 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 ASN A 11 20.38 -140.75 REMARK 500 THR A 14 74.00 60.72 REMARK 500 ASP A 50 48.54 -85.76 REMARK 500 LEU A 94 139.76 -171.03 REMARK 500 ALA A 132 69.07 -153.77 REMARK 500 SER A 140 -4.02 77.56 REMARK 500 ASN A 159 98.03 -162.43 REMARK 500 THR B 14 77.76 68.36 REMARK 500 ALA B 132 70.35 -155.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 IN THE INHIBITOR THE CH2-OH SIDE-CHAIN IN POSITION 6 IS REMARK 600 MOST LIKELY REPLACED BY OXYGEN. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ROI A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ROI B 602 DBREF 1CBK A 1 160 UNP P43777 HPPK_HAEIN 9 168 DBREF 1CBK B 1 160 UNP P43777 HPPK_HAEIN 9 168 SEQRES 1 A 160 MET ILE THR ALA TYR ILE ALA LEU GLY SER ASN LEU ASN SEQRES 2 A 160 THR PRO VAL GLU GLN LEU HIS ALA ALA LEU LYS ALA ILE SEQRES 3 A 160 SER GLN LEU SER ASN THR HIS LEU VAL THR THR SER SER SEQRES 4 A 160 PHE TYR LYS SER LYS PRO LEU GLY PRO GLN ASP GLN PRO SEQRES 5 A 160 ASP TYR VAL ASN ALA VAL ALA LYS ILE GLU THR GLU LEU SEQRES 6 A 160 SER PRO LEU LYS LEU LEU ASP GLU LEU GLN ARG ILE GLU SEQRES 7 A 160 ASN GLU GLN GLY ARG VAL ARG LEU ARG ARG TRP GLY GLU SEQRES 8 A 160 ARG THR LEU ASP LEU ASP ILE LEU LEU TYR GLY ASN GLU SEQRES 9 A 160 ILE ILE GLN ASN GLU ARG LEU THR ILE PRO HIS TYR ASP SEQRES 10 A 160 MET HIS ASN ARG GLU PHE VAL ILE VAL PRO LEU PHE GLU SEQRES 11 A 160 ILE ALA SER ASP LEU VAL LEU PRO ASN SER GLN ILE ILE SEQRES 12 A 160 THR GLU LEU VAL LYS GLN PHE ALA ASP HIS LYS MET ILE SEQRES 13 A 160 LYS LEU ASN PRO SEQRES 1 B 160 MET ILE THR ALA TYR ILE ALA LEU GLY SER ASN LEU ASN SEQRES 2 B 160 THR PRO VAL GLU GLN LEU HIS ALA ALA LEU LYS ALA ILE SEQRES 3 B 160 SER GLN LEU SER ASN THR HIS LEU VAL THR THR SER SER SEQRES 4 B 160 PHE TYR LYS SER LYS PRO LEU GLY PRO GLN ASP GLN PRO SEQRES 5 B 160 ASP TYR VAL ASN ALA VAL ALA LYS ILE GLU THR GLU LEU SEQRES 6 B 160 SER PRO LEU LYS LEU LEU ASP GLU LEU GLN ARG ILE GLU SEQRES 7 B 160 ASN GLU GLN GLY ARG VAL ARG LEU ARG ARG TRP GLY GLU SEQRES 8 B 160 ARG THR LEU ASP LEU ASP ILE LEU LEU TYR GLY ASN GLU SEQRES 9 B 160 ILE ILE GLN ASN GLU ARG LEU THR ILE PRO HIS TYR ASP SEQRES 10 B 160 MET HIS ASN ARG GLU PHE VAL ILE VAL PRO LEU PHE GLU SEQRES 11 B 160 ILE ALA SER ASP LEU VAL LEU PRO ASN SER GLN ILE ILE SEQRES 12 B 160 THR GLU LEU VAL LYS GLN PHE ALA ASP HIS LYS MET ILE SEQRES 13 B 160 LYS LEU ASN PRO HET SO4 A 501 5 HET ROI A 601 15 HET SO4 B 502 5 HET ROI B 602 15 HETNAM SO4 SULFATE ION HETNAM ROI 7,8-DIHYDRO-7,7-DIMETHYL-6-HYDROXYPTERIN FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 ROI 2(C8 H11 N5 O2) FORMUL 7 HOH *404(H2 O) HELIX 1 1 PRO A 15 SER A 27 1 13 HELIX 2 2 PRO A 67 GLU A 80 1 14 HELIX 3 3 TYR A 116 ASN A 120 5 5 HELIX 4 4 GLU A 122 ILE A 131 1 10 HELIX 5 5 ILE A 143 PHE A 150 1 8 HELIX 6 6 PRO B 15 SER B 27 1 13 HELIX 7 7 PRO B 67 GLU B 80 1 14 HELIX 8 8 TYR B 116 ASN B 120 5 5 HELIX 9 9 GLU B 122 ILE B 131 1 10 HELIX 10 10 ILE B 143 PHE B 150 1 8 SHEET 1 A 4 TYR A 41 SER A 43 0 SHEET 2 A 4 TYR A 54 THR A 63 -1 N ASN A 56 O TYR A 41 SHEET 3 A 4 ILE A 2 SER A 10 -1 N SER A 10 O VAL A 55 SHEET 4 A 4 ASP A 95 TYR A 101 -1 N LEU A 100 O TYR A 5 SHEET 1 B 2 THR A 32 THR A 37 0 SHEET 2 B 2 ALA A 59 THR A 63 -1 N GLU A 62 O HIS A 33 SHEET 1 C 4 TYR B 41 SER B 43 0 SHEET 2 C 4 TYR B 54 THR B 63 -1 N ASN B 56 O TYR B 41 SHEET 3 C 4 ILE B 2 SER B 10 -1 N SER B 10 O VAL B 55 SHEET 4 C 4 ASP B 95 TYR B 101 -1 N LEU B 100 O TYR B 5 SHEET 1 D 2 THR B 32 THR B 37 0 SHEET 2 D 2 ALA B 59 THR B 63 -1 N GLU B 62 O HIS B 33 CISPEP 1 ILE A 113 PRO A 114 0 -1.04 CISPEP 2 ASN A 159 PRO A 160 0 1.73 CISPEP 3 ILE B 113 PRO B 114 0 -0.02 CISPEP 4 ASN B 159 PRO B 160 0 0.74 SITE 1 AC1 7 ARG A 85 ARG A 88 TRP A 89 ARG A 92 SITE 2 AC1 7 HOH A 713 HOH A 716 HOH A 738 SITE 1 AC2 8 ARG B 85 ARG B 88 TRP B 89 ARG B 92 SITE 2 AC2 8 HOH B 618 HOH B 628 HOH B 631 HOH B 732 SITE 1 AC3 12 SER A 43 LYS A 44 LEU A 46 TYR A 54 SITE 2 AC3 12 ASN A 56 TRP A 89 ARG A 92 ASP A 95 SITE 3 AC3 12 PHE A 123 HOH A 683 HOH A 713 HOH A 743 SITE 1 AC4 11 SER B 43 LYS B 44 LEU B 46 TYR B 54 SITE 2 AC4 11 ASN B 56 TRP B 89 ARG B 92 ASP B 95 SITE 3 AC4 11 PHE B 123 HOH B 624 HOH B 631 CRYST1 112.775 50.791 70.893 90.00 101.73 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008867 0.000000 0.001841 0.00000 SCALE2 0.000000 0.019688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014407 0.00000