HEADER CYTOSOLIC PROTEIN 29-JUN-20 7CFZ TITLE SH3 DOMAIN OF NADPH OXIDASE ACTIVATOR 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADPH OXIDASE ACTIVATOR 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NOX ACTIVATOR 1,ANTIGEN NY-CO-31,NCF2-LIKE PROTEIN,P67PHOX- COMPND 5 LIKE FACTOR,P51-NOX; 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 GENE: NOXA1, P51NOX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SH3, NOXA1, NADPH OXIDASE ACTIVATOR 1, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KIM,J.H.PARK,P.ATTRI,W.LEE REVDAT 3 29-NOV-23 7CFZ 1 REMARK REVDAT 2 19-JAN-22 7CFZ 1 JRNL REVDAT 1 07-JUL-21 7CFZ 0 JRNL AUTH P.ATTRI,J.H.PARK,J.DE BACKER,M.KIM,J.H.YUN,Y.HEO,S.DEWILDE, JRNL AUTH 2 M.SHIRATANI,E.H.CHOI,W.LEE,A.BOGAERTS JRNL TITL STRUCTURAL MODIFICATION OF NADPH OXIDASE ACTIVATOR (NOXA 1) JRNL TITL 2 BY OXIDATIVE STRESS: AN EXPERIMENTAL AND COMPUTATIONAL JRNL TITL 3 STUDY. JRNL REF INT.J.BIOL.MACROMOL. V. 163 2405 2020 JRNL REFN ISSN 0141-8130 JRNL PMID 32961197 JRNL DOI 10.1016/J.IJBIOMAC.2020.09.120 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13-2998 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 9196 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 920 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 40.6800 - 3.6100 0.97 1253 139 0.2122 0.2333 REMARK 3 2 3.6100 - 2.8600 0.98 1198 134 0.2228 0.2578 REMARK 3 3 2.8600 - 2.5000 0.98 1171 130 0.2468 0.2758 REMARK 3 4 2.5000 - 2.2700 0.99 1171 130 0.2295 0.2993 REMARK 3 5 2.2700 - 2.1100 0.99 1173 130 0.2433 0.2798 REMARK 3 6 2.1100 - 1.9800 1.00 1160 130 0.2534 0.2525 REMARK 3 7 1.9800 - 1.8900 0.99 1150 127 0.2714 0.2798 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.219 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.303 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.39 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 933 REMARK 3 ANGLE : 0.695 1270 REMARK 3 CHIRALITY : 0.051 135 REMARK 3 PLANARITY : 0.004 170 REMARK 3 DIHEDRAL : 3.067 539 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7CFZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1300017535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 1.13_2998 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9201 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.885 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.64200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.13_2998 REMARK 200 STARTING MODEL: 5K28 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 0.2M MAGNESIUM REMARK 280 CHLORIDE HEXAHYDRATE, 25% PEG 3,350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.50700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.43400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.50700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.43400 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 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 121 LIES ON A SPECIAL POSITION. 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 GLY A 61 REMARK 465 PRO A 62 REMARK 465 ARG A 63 REMARK 465 MET A 64 REMARK 465 SER A 65 REMARK 465 GLY B 1 REMARK 465 ARG B 2 REMARK 465 GLY B 61 REMARK 465 PRO B 62 REMARK 465 ARG B 63 REMARK 465 MET B 64 REMARK 465 SER B 65 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 OE1 GLN A 17 O HOH A 101 2.14 REMARK 500 O HOH A 102 O HOH A 121 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 112 O HOH B 123 2565 2.19 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 ASP B 37 -174.95 55.96 REMARK 500 REMARK 500 REMARK: NULL DBREF 7CFZ A 1 65 UNP Q86UR1 NOXA1_HUMAN 397 461 DBREF 7CFZ B 1 65 UNP Q86UR1 NOXA1_HUMAN 397 461 SEQRES 1 A 65 GLY ARG PRO VAL LEU TYR GLN VAL VAL ALA GLN HIS SER SEQRES 2 A 65 TYR SER ALA GLN GLY PRO GLU ASP LEU GLY PHE ARG GLN SEQRES 3 A 65 GLY ASP THR VAL ASP VAL LEU CYS GLU VAL ASP GLN ALA SEQRES 4 A 65 TRP LEU GLU GLY HIS CYS ASP GLY ARG ILE GLY ILE PHE SEQRES 5 A 65 PRO LYS CYS PHE VAL VAL PRO ALA GLY PRO ARG MET SER SEQRES 1 B 65 GLY ARG PRO VAL LEU TYR GLN VAL VAL ALA GLN HIS SER SEQRES 2 B 65 TYR SER ALA GLN GLY PRO GLU ASP LEU GLY PHE ARG GLN SEQRES 3 B 65 GLY ASP THR VAL ASP VAL LEU CYS GLU VAL ASP GLN ALA SEQRES 4 B 65 TRP LEU GLU GLY HIS CYS ASP GLY ARG ILE GLY ILE PHE SEQRES 5 B 65 PRO LYS CYS PHE VAL VAL PRO ALA GLY PRO ARG MET SER FORMUL 3 HOH *48(H2 O) SHEET 1 AA1 5 ARG A 48 PRO A 53 0 SHEET 2 AA1 5 TRP A 40 CYS A 45 -1 N GLY A 43 O GLY A 50 SHEET 3 AA1 5 THR A 29 CYS A 34 -1 N LEU A 33 O GLU A 42 SHEET 4 AA1 5 TYR A 6 ALA A 10 -1 N VAL A 8 O VAL A 30 SHEET 5 AA1 5 VAL A 57 PRO A 59 -1 O VAL A 58 N VAL A 9 SHEET 1 AA2 5 ARG B 48 PRO B 53 0 SHEET 2 AA2 5 TRP B 40 CYS B 45 -1 N GLY B 43 O GLY B 50 SHEET 3 AA2 5 THR B 29 CYS B 34 -1 N CYS B 34 O GLU B 42 SHEET 4 AA2 5 TYR B 6 ALA B 10 -1 N VAL B 8 O VAL B 30 SHEET 5 AA2 5 VAL B 57 PRO B 59 -1 O VAL B 58 N VAL B 9 CRYST1 30.596 49.014 72.868 90.00 90.00 90.00 P 2 21 21 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 0.032684 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013723 0.00000 MASTER 276 0 0 0 10 0 0 6 957 2 0 10 END