HEADER SIGNALING PROTEIN 22-OCT-17 6BDE TITLE CRYSTAL STRUCTURE OF FE(II) UNLIGANDED H-NOX PROTEIN MUTANT A71G FROM TITLE 2 K. ALGICIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KORDIA ALGICIDA OT-1; SOURCE 3 ORGANISM_TAXID: 391587; SOURCE 4 GENE: KAOT1_17313; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NITRIC OXIDE SIGNALING, HEME NITRIC OXIDE/OXYGEN SENSING PROTEIN, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.J.BRUEGGER,C.W.HESPEN,M.A.MARLETTA REVDAT 3 04-OCT-23 6BDE 1 REMARK REVDAT 2 27-JUN-18 6BDE 1 JRNL REVDAT 1 30-MAY-18 6BDE 0 JRNL AUTH C.W.HESPEN,J.J.BRUEGGER,Y.GUO,M.A.MARLETTA JRNL TITL NATIVE ALANINE SUBSTITUTION IN THE GLYCINE HINGE MODULATES JRNL TITL 2 CONFORMATIONAL FLEXIBILITY OF HEME NITRIC OXIDE/OXYGEN JRNL TITL 3 (H-NOX) SENSING PROTEINS. JRNL REF ACS CHEM. BIOL. V. 13 1631 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 29757599 JRNL DOI 10.1021/ACSCHEMBIO.8B00248 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 23631 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1183 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 39.8031 - 3.2819 0.98 2944 165 0.1821 0.2000 REMARK 3 2 3.2819 - 2.6051 1.00 2861 163 0.2304 0.2793 REMARK 3 3 2.6051 - 2.2758 1.00 2865 127 0.2257 0.2463 REMARK 3 4 2.2758 - 2.0678 1.00 2832 154 0.2276 0.2319 REMARK 3 5 2.0678 - 1.9196 1.00 2797 151 0.2333 0.2746 REMARK 3 6 1.9196 - 1.8064 1.00 2821 142 0.2534 0.3101 REMARK 3 7 1.8064 - 1.7159 1.00 2789 135 0.2649 0.2861 REMARK 3 8 1.7159 - 1.6412 0.91 2539 146 0.2864 0.3573 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.46 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 : 0.005 1575 REMARK 3 ANGLE : 2.816 2139 REMARK 3 CHIRALITY : 0.040 235 REMARK 3 PLANARITY : 0.003 267 REMARK 3 DIHEDRAL : 6.256 933 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 2.6513 -6.7623 -1.8656 REMARK 3 T TENSOR REMARK 3 T11: 0.2267 T22: 0.2843 REMARK 3 T33: 0.2305 T12: -0.0257 REMARK 3 T13: -0.0480 T23: 0.0248 REMARK 3 L TENSOR REMARK 3 L11: 4.3661 L22: 1.7139 REMARK 3 L33: 2.4037 L12: -0.0623 REMARK 3 L13: 0.1251 L23: 0.2128 REMARK 3 S TENSOR REMARK 3 S11: -0.1545 S12: 0.3779 S13: 0.2852 REMARK 3 S21: -0.0619 S22: -0.0740 S23: 0.1034 REMARK 3 S31: -0.1507 S32: 0.0160 S33: 0.1907 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 6BDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230705. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23704 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6BDD REMARK 200 REMARK 200 REMARK: ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 8.5, 0.3 M LICL, REMARK 280 34% PEG 6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.39700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.37650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.36500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.37650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.39700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.36500 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: PISA 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 LEU A 31 78.58 93.20 REMARK 500 HIS A 102 -61.35 -139.46 REMARK 500 MET A 139 43.92 -98.17 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 A 425 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 426 DISTANCE = 6.69 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 104 NE2 REMARK 620 2 HEM A 201 NA 109.1 REMARK 620 3 HEM A 201 NB 105.3 84.5 REMARK 620 4 HEM A 201 NC 101.3 149.6 87.3 REMARK 620 5 HEM A 201 ND 106.1 84.6 148.6 87.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6BDD RELATED DB: PDB DBREF 6BDE A 1 179 UNP A9DSJ8 A9DSJ8_9FLAO 1 179 SEQADV 6BDE GLY A 71 UNP A9DSJ8 ALA 71 ENGINEERED MUTATION SEQADV 6BDE GLU A 180 UNP A9DSJ8 EXPRESSION TAG SEQADV 6BDE ASN A 181 UNP A9DSJ8 EXPRESSION TAG SEQADV 6BDE LEU A 182 UNP A9DSJ8 EXPRESSION TAG SEQADV 6BDE TYR A 183 UNP A9DSJ8 EXPRESSION TAG SEQADV 6BDE PHE A 184 UNP A9DSJ8 EXPRESSION TAG SEQADV 6BDE GLN A 185 UNP A9DSJ8 EXPRESSION TAG SEQRES 1 A 185 MET LYS GLY ILE ILE PHE THR GLU PHE LEU ASP LEU VAL SEQRES 2 A 185 GLU ASP LYS PHE GLY LEU GLU MET VAL ASP LYS ILE ILE SEQRES 3 A 185 THR GLN SER GLU LEU GLU SER GLU GLY VAL TYR THR SER SEQRES 4 A 185 ILE GLY THR TYR ARG PHE SER GLU MET LEU GLN LEU LEU SEQRES 5 A 185 GLN ASN LEU SER ALA ASN THR ASP VAL SER ILE ASP ASP SEQRES 6 A 185 LEU LEU LEU THR TYR GLY GLU HIS PHE PHE SER VAL ILE SEQRES 7 A 185 GLU ASP SER TYR PRO GLY LEU LEU ALA THR TYR LYS ASP SEQRES 8 A 185 PRO ILE GLU MET LEU ALA SER ILE GLU ASN HIS ILE HIS SEQRES 9 A 185 VAL GLU VAL ARG LYS ILE TYR PRO ASP ALA GLU LEU PRO SEQRES 10 A 185 THR PHE VAL VAL GLU GLU LYS THR ALA ASN SER LEU THR SEQRES 11 A 185 MET ILE TYR LYS SER SER ARG ALA MET HIS HIS PHE GLY SEQRES 12 A 185 LEU GLY LEU MET ASN LYS THR PHE GLU HIS PHE ASN SER SEQRES 13 A 185 SER ALA GLU ILE ILE LEU GLU LYS ILE LYS GLU ASP GLY SEQRES 14 A 185 THR GLU VAL LYS PHE ILE ILE ASN LYS ASN GLU ASN LEU SEQRES 15 A 185 TYR PHE GLN HET HEM A 201 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *126(H2 O) HELIX 1 AA1 LYS A 2 GLY A 18 1 17 HELIX 2 AA2 GLY A 18 GLN A 28 1 11 HELIX 3 AA3 ARG A 44 ASP A 60 1 17 HELIX 4 AA4 SER A 62 TYR A 82 1 21 HELIX 5 AA5 TYR A 82 THR A 88 1 7 HELIX 6 AA6 ASP A 91 ALA A 97 1 7 HELIX 7 AA7 HIS A 102 TYR A 111 1 10 HELIX 8 AA8 MET A 139 PHE A 154 1 16 SHEET 1 AA1 4 THR A 118 LYS A 124 0 SHEET 2 AA1 4 SER A 128 LYS A 134 -1 O THR A 130 N GLU A 122 SHEET 3 AA1 4 GLU A 171 LYS A 178 -1 O VAL A 172 N TYR A 133 SHEET 4 AA1 4 ALA A 158 LYS A 164 -1 N GLU A 163 O LYS A 173 LINK NE2 HIS A 104 FE HEM A 201 1555 1555 2.00 CISPEP 1 GLU A 30 LEU A 31 0 3.46 SITE 1 AC1 23 MET A 1 LYS A 2 ILE A 5 ILE A 78 SITE 2 AC1 23 LEU A 85 ILE A 99 ILE A 103 HIS A 104 SITE 3 AC1 23 VAL A 107 ALA A 114 GLU A 115 LEU A 116 SITE 4 AC1 23 PRO A 117 PHE A 119 TYR A 133 SER A 135 SITE 5 AC1 23 ARG A 137 MET A 139 PHE A 142 GLY A 143 SITE 6 AC1 23 LEU A 146 MET A 147 HOH A 351 CRYST1 48.794 56.730 68.753 90.00 90.00 90.00 P 21 21 21 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 0.020494 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017627 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014545 0.00000