HEADER ELECTRON TRANSPORT 15-SEP-00 1FUE TITLE FLAVODOXIN FROM HELICOBACTER PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVODOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PTYB1 KEYWDS FLAVOPROTEIN, HELICOBACTER PYLORI, FMN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.FREIGANG,K.DIEDERICHS,K.P.SCHAEFER,W.WELTE,R.PAUL REVDAT 5 07-FEB-24 1FUE 1 REMARK REVDAT 4 04-APR-18 1FUE 1 REMARK REVDAT 3 24-FEB-09 1FUE 1 VERSN REVDAT 2 01-APR-03 1FUE 1 JRNL REVDAT 1 06-FEB-02 1FUE 0 JRNL AUTH J.FREIGANG,K.DIEDERICHS,K.P.SCHAFER,W.WELTE,R.PAUL JRNL TITL CRYSTAL STRUCTURE OF OXIDIZED FLAVODOXIN, AN ESSENTIAL JRNL TITL 2 PROTEIN IN HELICOBACTER PYLORI. JRNL REF PROTEIN SCI. V. 11 253 2002 JRNL REFN ISSN 0961-8368 JRNL PMID 11790835 JRNL DOI 10.1110/PS.28602 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 271006.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 5144 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) : 0.198 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 536 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 738 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 85 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.034 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1222 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 32 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -14.86000 REMARK 3 B22 (A**2) : 4.22000 REMARK 3 B33 (A**2) : 10.63000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.97000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.36 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) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.660 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) : 3.080 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.720 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.580 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.570 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.29 REMARK 3 BSOL : 41.65 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.PARAM REMARK 3 PARAMETER FILE 3 : FMN.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : FMN.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FUE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000011911. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5346 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -10.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 2.460 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.48 REMARK 200 R MERGE FOR SHELL (I) : 0.32500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1500, PH 7, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 290K 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 23.61000 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: 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 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 ALA A 57 -7.32 76.61 REMARK 500 GLU A 94 51.04 -117.33 REMARK 500 THR A 95 22.50 178.22 REMARK 500 PHE A 96 109.15 -58.35 REMARK 500 ALA A 124 -69.65 -90.51 REMARK 500 SER A 126 116.01 179.70 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 FMN A 165 DBREF 1FUE A 2 164 UNP Q9ZK53 FLAV_HELPJ 2 164 SEQADV 1FUE VAL A 32 UNP Q9ZK53 ILE 32 SEE REMARK 999 SEQADV 1FUE SER A 117 UNP Q9ZK53 PRO 117 SEE REMARK 999 SEQADV 1FUE ALA A 124 UNP Q9ZK53 GLU 124 SEE REMARK 999 SEQADV 1FUE ARG A 160 UNP Q9ZK53 LYS 160 SEE REMARK 999 SEQRES 1 A 163 GLY LYS ILE GLY ILE PHE PHE GLY THR ASP SER GLY ASN SEQRES 2 A 163 ALA GLU ALA ILE ALA GLU LYS ILE SER LYS ALA ILE GLY SEQRES 3 A 163 ASN ALA GLU VAL VAL ASP VAL ALA LYS ALA SER LYS GLU SEQRES 4 A 163 GLN PHE ASN GLY PHE THR LYS VAL ILE LEU VAL ALA PRO SEQRES 5 A 163 THR ALA GLY ALA GLY ASP LEU GLN THR ASP TRP GLU ASP SEQRES 6 A 163 PHE LEU GLY THR LEU GLU ALA SER ASP PHE ALA ASN LYS SEQRES 7 A 163 THR ILE GLY LEU VAL GLY LEU GLY ASP GLN ASP THR TYR SEQRES 8 A 163 SER GLU THR PHE ALA GLU GLY ILE PHE HIS ILE TYR GLU SEQRES 9 A 163 LYS ALA LYS ALA GLY LYS VAL VAL GLY GLN THR SER THR SEQRES 10 A 163 ASP GLY TYR HIS PHE ALA ALA SER LYS ALA VAL GLU GLY SEQRES 11 A 163 GLY LYS PHE VAL GLY LEU VAL ILE ASP GLU ASP ASN GLN SEQRES 12 A 163 ASP ASP LEU THR ASP GLU ARG ILE ALA LYS TRP VAL GLU SEQRES 13 A 163 GLN VAL ARG GLY SER PHE ALA HET FMN A 165 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 HOH *32(H2 O) HELIX 1 1 GLY A 13 GLY A 27 1 15 HELIX 2 2 ALA A 35 ALA A 37 5 3 HELIX 3 3 SER A 38 ASN A 43 1 6 HELIX 4 4 ALA A 55 ASP A 59 5 5 HELIX 5 5 GLN A 61 GLY A 69 1 9 HELIX 6 6 THR A 70 LEU A 71 5 2 HELIX 7 7 GLU A 72 GLU A 72 5 1 HELIX 8 8 ALA A 73 ASN A 78 1 6 HELIX 9 9 GLU A 98 LYS A 108 1 11 HELIX 10 10 GLN A 144 ASP A 146 5 3 HELIX 11 11 LEU A 147 GLY A 161 1 15 SHEET 1 A 5 ALA A 29 ASP A 33 0 SHEET 2 A 5 ILE A 4 PHE A 8 1 O ILE A 4 N GLU A 30 SHEET 3 A 5 LYS A 47 PRO A 53 1 O LYS A 47 N GLY A 5 SHEET 4 A 5 THR A 80 LEU A 86 1 O THR A 80 N VAL A 48 SHEET 5 A 5 LYS A 111 VAL A 112 1 O LYS A 111 N ILE A 81 SHEET 1 B 5 ALA A 29 ASP A 33 0 SHEET 2 B 5 ILE A 4 PHE A 8 1 O ILE A 4 N GLU A 30 SHEET 3 B 5 LYS A 47 PRO A 53 1 O LYS A 47 N GLY A 5 SHEET 4 B 5 THR A 80 LEU A 86 1 O THR A 80 N VAL A 48 SHEET 5 B 5 LEU A 137 ILE A 139 1 O LEU A 137 N GLY A 85 SITE 1 AC1 22 THR A 10 ASP A 11 SER A 12 GLY A 13 SITE 2 AC1 22 ASN A 14 ALA A 15 PRO A 53 THR A 54 SITE 3 AC1 22 ALA A 55 GLY A 56 ALA A 57 GLY A 58 SITE 4 AC1 22 LEU A 86 GLY A 87 ASP A 88 TYR A 92 SITE 5 AC1 22 THR A 95 PHE A 96 ALA A 97 ASP A 142 SITE 6 AC1 22 HOH A 202 HOH A 217 CRYST1 31.130 47.220 48.310 90.00 97.14 90.00 P 1 21 1 2 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 0.032123 0.000000 0.004024 0.00000 SCALE2 0.000000 0.021177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020861 0.00000