PDB Short entry for 1H6H HEADER PX DOMAIN 15-JUN-01 1H6H TITLE STRUCTURE OF THE PX DOMAIN FROM P40PHOX BOUND TO PHOSPHATIDYLINOSITOL TITLE 2 3-PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL CYTOSOL FACTOR 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PX DOMAIN RESIDUES 2-144; COMPND 5 SYNONYM: NCF-4, NEUTROPHIL NADPH OXIDASE FACTOR 4, P40-PHOX, P40PHOX; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: NEUTROPHIL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE KEYWDS PX DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR D.KARATHANASSIS,J.BRAVO,M.PACOLD,O.PERISIC,R.L.WILLIAMS REVDAT 3 24-JAN-18 1H6H 1 SOURCE REVDAT 2 24-FEB-09 1H6H 1 VERSN REVDAT 1 01-NOV-01 1H6H 0 JRNL AUTH J.BRAVO,D.KARATHANASSIS,C.M.PACOLD,M.E.PACOLD,C.D.ELLSON, JRNL AUTH 2 K.E.ANDERSON,J.G.BUTLER,I.LAVENIR,O.PERISIC,P.T.HAWKINS, JRNL AUTH 3 L.STEPHENS,R.L.WILLIAMS JRNL TITL THE CRYSTAL STRUCTURE OF THE PX DOMAIN FROM P40PHOX BOUND TO JRNL TITL 2 PHOSPHATIDYLINOSITOL 3-PHOSPHATE JRNL REF MOL.CELL V. 8 829 2001 JRNL REFN ISSN 1097-2765 JRNL PMID 11684018 JRNL DOI 10.1016/S1097-2765(01)00372-0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.HIROAKI,T.AGO,T.ITO,H.SUMIMOTO,D.KOHDA REMARK 1 TITL SOLUTION STRUCTURE OF THE PX DOMAIN, A TARGET OF THE SH3 REMARK 1 TITL 2 DOMAIN REMARK 1 REF NAT.STRUCT.BIOL. V. 8 526 2001 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 11373621 REMARK 1 DOI 10.1038/88591 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1091987.270 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 18117 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) : 0.196 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 921 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 50.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1620 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1150 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.02000 REMARK 3 B22 (A**2) : -3.54000 REMARK 3 B33 (A**2) : 4.55000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.47000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.980 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) : 1.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.230 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.970 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.950 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 49.48 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 : I3P.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : GOL.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : I3P.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 4 : GOL.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1H6H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1290008143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : SI CRYSTAL REMARK 200 OPTICS : RH COATED SI MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18117 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 56.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : 0.15600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.50 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 48.38000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.82100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.38000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.82100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 SER A 79 33.30 -158.30 REMARK 500 SER A 80 -46.53 -12.71 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 PIB A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 151 DBREF 1H6H A 2 144 UNP Q15080 NCF4_HUMAN 2 144 SEQRES 1 A 143 ALA VAL ALA GLN GLN LEU ARG ALA GLU SER ASP PHE GLU SEQRES 2 A 143 GLN LEU PRO ASP ASP VAL ALA ILE SER ALA ASN ILE ALA SEQRES 3 A 143 ASP ILE GLU GLU LYS ARG GLY PHE THR SER HIS PHE VAL SEQRES 4 A 143 PHE VAL ILE GLU VAL LYS THR LYS GLY GLY SER LYS TYR SEQRES 5 A 143 LEU ILE TYR ARG ARG TYR ARG GLN PHE HIS ALA LEU GLN SEQRES 6 A 143 SER LYS LEU GLU GLU ARG PHE GLY PRO ASP SER LYS SER SEQRES 7 A 143 SER ALA LEU ALA CYS THR LEU PRO THR LEU PRO ALA LYS SEQRES 8 A 143 VAL TYR VAL GLY VAL LYS GLN GLU ILE ALA GLU MET ARG SEQRES 9 A 143 ILE PRO ALA LEU ASN ALA TYR MET LYS SER LEU LEU SER SEQRES 10 A 143 LEU PRO VAL TRP VAL LEU MET ASP GLU ASP VAL ARG ILE SEQRES 11 A 143 PHE PHE TYR GLN SER PRO TYR ASP SER GLU GLN VAL PRO HET PIB A 150 35 HET GOL A 151 6 HETNAM PIB 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5- HETNAM 2 PIB (PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL) HETNAM 3 PIB OXY]METHYL}ETHYL BUTANOATE HETNAM GOL GLYCEROL HETSYN PIB D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATED (+)-SN-1,2-DI- HETSYN 2 PIB O-BUTANOYLGLYCERYL,3-O-PHOSPHO HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PIB C17 H32 O16 P2 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *182(H2 O) HELIX 1 1 ALA A 2 LEU A 16 1 15 HELIX 2 2 TYR A 59 GLY A 74 1 16 HELIX 3 3 SER A 79 ALA A 83 5 5 HELIX 4 4 VAL A 97 LEU A 117 1 21 HELIX 5 5 PRO A 120 MET A 125 1 6 HELIX 6 6 ASP A 126 TYR A 134 1 9 HELIX 7 7 SER A 136 GLU A 141 1 6 SHEET 1 AA 3 ALA A 21 LYS A 32 0 SHEET 2 AA 3 HIS A 38 THR A 47 -1 O HIS A 38 N LYS A 32 SHEET 3 AA 3 LYS A 52 ARG A 58 -1 O TYR A 53 N VAL A 45 SITE 1 AC1 21 ILE A 26 ALA A 27 ARG A 58 TYR A 59 SITE 2 AC1 21 ARG A 60 LYS A 92 VAL A 93 TYR A 94 SITE 3 AC1 21 ARG A 105 HOH A2057 HOH A2170 HOH A2171 SITE 4 AC1 21 HOH A2172 HOH A2173 HOH A2174 HOH A2175 SITE 5 AC1 21 HOH A2176 HOH A2177 HOH A2178 HOH A2179 SITE 6 AC1 21 HOH A2180 SITE 1 AC2 7 ILE A 29 GLU A 30 GLU A 31 GLN A 99 SITE 2 AC2 7 HOH A2038 HOH A2041 HOH A2181 CRYST1 96.760 33.642 76.430 90.00 132.42 90.00 C 1 2 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 0.010335 0.000000 0.009444 0.00000 SCALE2 0.000000 0.029725 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017724 0.00000