HEADER SH3 DOMAIN 24-AUG-04 1W6X TITLE SH3 DOMAIN OF P40PHOX, COMPONENT OF THE NADPH OXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL CYTOSOL FACTOR 4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SH3 DOMAIN, RESIDUES 174-228; COMPND 5 SYNONYM: NCF-4, NEUTROPHIL NADPH OXIDASE FACTOR 4, P40PHOX, P40-PHOX; 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: NEUTROPHILE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PIVEX2.4 KEYWDS NADPH OXIDASE, P40PHOX, PHAGOCYTE, SH3 DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR C.MASSENET,S.CHENAVAS,C.COHEN-ADDAD,M.-C.DAGHER,G.BRANDOLIN,E.PEBAY- AUTHOR 2 PEYROULA,F.FIESCHI REVDAT 6 08-MAY-19 1W6X 1 REMARK REVDAT 5 06-MAR-19 1W6X 1 REMARK REVDAT 4 13-JUN-18 1W6X 1 JRNL REVDAT 3 24-FEB-09 1W6X 1 VERSN REVDAT 2 04-APR-05 1W6X 1 JRNL REVDAT 1 18-JAN-05 1W6X 0 JRNL AUTH C.MASSENET,S.CHENAVAS,C.COHEN-ADDAD,M.-C.DAGHER,G.BRANDOLIN, JRNL AUTH 2 E.PEBAY-PEYROULA,F.FIESCHI JRNL TITL EFFECTS OF P47PHOX C-TERMINUS PHOSPHORYLATION ON BINDING JRNL TITL 2 INTERACTIONS WITH P40PHOX AND P67PHOX: STRUCTURAL AND JRNL TITL 3 FUNCTIONAL COMPARISON OF P40PHOX P67PHOX SH3 DOMAINS JRNL REF J.BIOL.CHEM. V. 280 13752 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15657040 JRNL DOI 10.1074/JBC.M412897200 REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 6871 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) : 0.248 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 356 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 : 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) (%) : 92.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 607 REMARK 3 BIN R VALUE (WORKING SET) : 0.3511 REMARK 3 BIN FREE R VALUE : 0.4380 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.36 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 45 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 : 882 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41700 REMARK 3 B22 (A**2) : 4.57900 REMARK 3 B33 (A**2) : -4.16200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 11.02800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.32 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) : 0.47 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.302 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.37 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.777 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 49.00 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 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1W6X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1290020869. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL 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 : NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6876 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.7000 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) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE STARTING MODEL CONSISTED OF A SUPERPOSITION OF 8 SH3 REMARK 200 STRUCTURES 1SEM, 1SHG, 1ABQ, 1FYN, 1I0C,1B07, 1BB9, 1BU1 USING REMARK 200 MAIN CHAIN ATOMS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION AT 14 DEGRE C, PROTEIN REMARK 280 AT 14 MG/ML, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 40% REMARK 280 PEG2K MME, 100 MM AS 200 MM NA AC PH 4.6., TEMPERATURE 287K 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 22.58000 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 LEU A 169 REMARK 465 ILE A 170 REMARK 465 LYS A 171 REMARK 465 HIS A 172 REMARK 465 LEU B 169 REMARK 465 ILE B 170 REMARK 465 LYS B 171 REMARK 465 HIS B 172 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 LYS A 205 CG CD CE NZ REMARK 470 LYS B 205 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 185 O HOH A 2010 0.00 REMARK 500 CB SER A 185 O HOH A 2010 1.41 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 SER A 201 167.40 167.69 REMARK 500 SER B 201 168.72 168.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2008 DISTANCE = 6.92 ANGSTROMS REMARK 525 HOH A2013 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH B2006 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH B2008 DISTANCE = 7.04 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H6H RELATED DB: PDB REMARK 900 STRUCTURE OF THE PX DOMAIN FROM P40PHOX BOUND TO REMARK 900 PHOSPHATIDYLINOSITOL 3-PHOSPHATE REMARK 900 RELATED ID: 1OEY RELATED DB: PDB REMARK 900 HETERODIMER OF P40PHOX AND P67PHOX PB1 DOMAINS FROM HUMAN NADPH REMARK 900 OXIDASE REMARK 900 RELATED ID: 1W70 RELATED DB: PDB REMARK 900 SH3 DOMAIN OF P40PHOX COMPLEXED WITH C- TERMINAL POLYPROLINE OF REMARK 900 P47PHOX, COMPONENTS OF THE NADPH OXIDASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE STRUCTURE CORRESPONDS ONLY TO THE SH3 DOMAIN DBREF 1W6X A 169 173 PDB 1W6X 1W6X 169 173 DBREF 1W6X A 174 228 UNP Q15080 NCF4_HUMAN 174 228 DBREF 1W6X B 169 173 PDB 1W6X 1W6X 169 173 DBREF 1W6X B 174 228 UNP Q15080 NCF4_HUMAN 174 228 SEQRES 1 A 60 LEU ILE LYS HIS MET ARG ALA GLU ALA LEU PHE ASP PHE SEQRES 2 A 60 THR GLY ASN SER LYS LEU GLU LEU ASN PHE LYS ALA GLY SEQRES 3 A 60 ASP VAL ILE PHE LEU LEU SER ARG ILE ASN LYS ASP TRP SEQRES 4 A 60 LEU GLU GLY THR VAL ARG GLY ALA THR GLY ILE PHE PRO SEQRES 5 A 60 LEU SER PHE VAL LYS ILE LEU LYS SEQRES 1 B 60 LEU ILE LYS HIS MET ARG ALA GLU ALA LEU PHE ASP PHE SEQRES 2 B 60 THR GLY ASN SER LYS LEU GLU LEU ASN PHE LYS ALA GLY SEQRES 3 B 60 ASP VAL ILE PHE LEU LEU SER ARG ILE ASN LYS ASP TRP SEQRES 4 B 60 LEU GLU GLY THR VAL ARG GLY ALA THR GLY ILE PHE PRO SEQRES 5 B 60 LEU SER PHE VAL LYS ILE LEU LYS FORMUL 3 HOH *61(H2 O) SHEET 1 AA 5 ALA A 215 PRO A 220 0 SHEET 2 AA 5 TRP A 207 VAL A 212 -1 O LEU A 208 N PHE A 219 SHEET 3 AA 5 VAL A 196 ASN A 204 -1 O PHE A 198 N THR A 211 SHEET 4 AA 5 ARG A 174 ALA A 177 -1 O ALA A 175 N ILE A 197 SHEET 5 AA 5 VAL A 224 LEU A 227 -1 O LYS A 225 N GLU A 176 SHEET 1 BA 5 ALA B 215 PRO B 220 0 SHEET 2 BA 5 TRP B 207 VAL B 212 -1 O LEU B 208 N PHE B 219 SHEET 3 BA 5 VAL B 196 ASN B 204 -1 O PHE B 198 N THR B 211 SHEET 4 BA 5 ARG B 174 ALA B 177 -1 O ALA B 175 N ILE B 197 SHEET 5 BA 5 VAL B 224 LEU B 227 -1 O LYS B 225 N GLU B 176 CRYST1 35.160 45.160 35.060 90.00 111.43 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 0.028441 0.000000 0.011163 0.00000 SCALE2 0.000000 0.022143 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030641 0.00000