HEADER SIGNALING PROTEIN 28-APR-20 6WQE TITLE SOLUTION STRUCTURE OF THE IWP-051-BOUND H-NOX FROM SHEWANELLA WOODYI TITLE 2 IN THE FE(II)CO LIGATION STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEME NO BINDING DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA WOODYI; SOURCE 3 ORGANISM_TAXID: 60961; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: TUNER PLYSS KEYWDS HEMOPROTEIN, NITRIC OXIDE, SIGNALING, SIGNALING PROTEIN, SGC KEYWDS 2 STIMULATOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.Y.CHEN,W.LEE,W.R.MONTFORT REVDAT 4 01-MAY-24 6WQE 1 REMARK REVDAT 3 03-MAR-21 6WQE 1 JRNL REVDAT 2 09-DEC-20 6WQE 1 JRNL REVDAT 1 22-JUL-20 6WQE 0 JRNL AUTH C.Y.CHEN,W.LEE,P.A.RENHOWE,J.JUNG,W.R.MONTFORT JRNL TITL SOLUTION STRUCTURES OF THE SHEWANELLA WOODYI H-NOX PROTEIN JRNL TITL 2 IN THE PRESENCE AND ABSENCE OF SOLUBLE GUANYLYL CYCLASE JRNL TITL 3 STIMULATOR IWP-051. JRNL REF PROTEIN SCI. V. 30 448 2021 JRNL REFN ESSN 1469-896X JRNL PMID 33236796 JRNL DOI 10.1002/PRO.4005 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE GEOMETRY,TORSION ANGLE REMARK 3 DYNAMICS,MOLECULAR DYNAMICS REMARK 4 REMARK 4 6WQE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000240479. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 293; 298 REMARK 210 PH : 7.4; 7.4; 7.4 REMARK 210 IONIC STRENGTH : 50; 50; 100 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 500 UM [U-99% 15N] PROTEIN, 2400 REMARK 210 UM LIGAND, 90% H2O/10% D2O; 600 REMARK 210 UM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN, 3500 UM LIGAND, 100% REMARK 210 D2O; 600 UM [U-99% 15N] PROTEIN, REMARK 210 3000 UM 13C LABELED ON THE REMARK 210 BENZENE CARBON LIGAND, 100% D2O; REMARK 210 15.0 UM PROTEIN, 292.0 UM LIGAND, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N TROSY; REMARK 210 2D 13C15NFILTERED NOESY; 2D 1H- REMARK 210 1H NOESY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AGILENT 800; AGILENT 600; AVANCE REMARK 210 NEO REMARK 210 SPECTROMETER MANUFACTURER : AGILENT; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, SPARKY, NMRPIPE, REMARK 210 VNMR, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: CLOSE CONTACTS 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 HG3 MET A 4 HB2 SER A 39 1.25 REMARK 500 HB3 TYR A 37 H THR A 38 1.25 REMARK 500 FE HEM A 502 C CMO A 503 1.90 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 1 MET A 2 -35.17 -151.73 REMARK 500 1 SER A 33 -141.62 -102.29 REMARK 500 1 TYR A 37 -132.47 -95.93 REMARK 500 1 VAL A 40 -5.04 177.06 REMARK 500 1 SER A 42 81.53 165.55 REMARK 500 1 TYR A 111 90.14 -171.36 REMARK 500 1 PRO A 117 -149.09 -86.97 REMARK 500 1 GLU A 156 -167.76 -104.65 REMARK 500 1 THR A 171 -37.79 84.62 REMARK 500 1 ARG A 182 -6.45 86.90 REMARK 500 1 TYR A 188 -108.05 -115.73 REMARK 500 2 MET A 2 -34.49 -152.56 REMARK 500 2 SER A 33 -140.01 -99.80 REMARK 500 2 TYR A 37 -137.47 -96.97 REMARK 500 2 VAL A 40 -5.11 177.50 REMARK 500 2 SER A 42 81.17 165.60 REMARK 500 2 TYR A 111 92.37 -169.86 REMARK 500 2 PRO A 117 -147.47 -87.85 REMARK 500 2 GLU A 156 -166.96 -104.99 REMARK 500 2 THR A 171 -37.49 84.61 REMARK 500 2 ARG A 182 -8.22 87.82 REMARK 500 2 ASN A 186 37.25 71.49 REMARK 500 2 TYR A 188 -108.01 -122.12 REMARK 500 3 MET A 2 -35.93 -151.48 REMARK 500 3 SER A 33 -142.16 -101.98 REMARK 500 3 TYR A 37 -135.09 -95.18 REMARK 500 3 VAL A 40 -4.81 177.31 REMARK 500 3 SER A 42 81.91 164.87 REMARK 500 3 TYR A 111 92.61 -170.52 REMARK 500 3 PRO A 117 -147.62 -87.88 REMARK 500 3 GLU A 156 -165.91 -106.63 REMARK 500 3 THR A 171 -38.02 85.11 REMARK 500 3 ARG A 182 -8.45 88.41 REMARK 500 3 TYR A 188 -109.65 -120.03 REMARK 500 4 MET A 2 -29.39 -149.56 REMARK 500 4 SER A 33 -140.01 -98.33 REMARK 500 4 TYR A 37 -140.96 -94.30 REMARK 500 4 VAL A 40 -0.75 176.65 REMARK 500 4 SER A 42 -176.55 -178.53 REMARK 500 4 TYR A 111 93.27 -168.92 REMARK 500 4 GLU A 156 -165.77 -107.33 REMARK 500 4 THR A 171 -53.01 153.83 REMARK 500 4 ARG A 182 -8.56 87.25 REMARK 500 4 ASN A 186 42.21 71.95 REMARK 500 4 TYR A 188 -115.34 -131.47 REMARK 500 5 MET A 2 -32.96 -148.55 REMARK 500 5 SER A 33 -140.84 -103.01 REMARK 500 5 TYR A 37 -140.51 -94.92 REMARK 500 5 VAL A 40 -7.87 -176.37 REMARK 500 5 TYR A 111 94.31 -171.99 REMARK 500 REMARK 500 THIS ENTRY HAS 231 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL 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 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 104 NE2 REMARK 620 2 HEM A 502 NA 95.5 REMARK 620 3 HEM A 502 NB 94.6 90.0 REMARK 620 4 HEM A 502 NC 85.7 178.8 89.7 REMARK 620 5 HEM A 502 ND 85.1 89.2 179.2 91.1 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 IWP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CMO A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6OCV RELATED DB: PDB REMARK 900 6OCV CONTAINS THE SAME PROTEIN IN ITS NATIVE STATE REMARK 900 RELATED ID: 27284 RELATED DB: BMRB DBREF 6WQE A 1 182 UNP B1KIH6 B1KIH6_SHEWM 1 182 SEQADV 6WQE GLY A 183 UNP B1KIH6 EXPRESSION TAG SEQADV 6WQE ALA A 184 UNP B1KIH6 EXPRESSION TAG SEQADV 6WQE GLU A 185 UNP B1KIH6 EXPRESSION TAG SEQADV 6WQE ASN A 186 UNP B1KIH6 EXPRESSION TAG SEQADV 6WQE LEU A 187 UNP B1KIH6 EXPRESSION TAG SEQADV 6WQE TYR A 188 UNP B1KIH6 EXPRESSION TAG SEQADV 6WQE PHE A 189 UNP B1KIH6 EXPRESSION TAG SEQADV 6WQE GLN A 190 UNP B1KIH6 EXPRESSION TAG SEQRES 1 A 190 MET MET GLY MET VAL PHE THR GLY LEU MET GLU LEU ILE SEQRES 2 A 190 GLU ASP GLU PHE GLY TYR GLU THR LEU ASP THR LEU LEU SEQRES 3 A 190 GLU SER CYS GLU LEU GLN SER GLU GLY ILE TYR THR SER SEQRES 4 A 190 VAL GLY SER TYR ASP HIS GLN GLU LEU LEU GLN LEU VAL SEQRES 5 A 190 VAL LYS LEU SER GLU VAL SER SER VAL PRO VAL THR GLU SEQRES 6 A 190 LEU VAL ARG LEU PHE GLY LYS LYS LEU PHE VAL GLU LEU SEQRES 7 A 190 ILE GLU GLY HIS PRO GLU ILE ALA ASN GLU MET LYS ASP SEQRES 8 A 190 SER PHE ASP LEU LEU SER LYS ILE ASP SER PHE ILE HIS SEQRES 9 A 190 VAL GLU VAL TYR LYS LEU TYR PRO GLN ALA GLU LEU PRO SEQRES 10 A 190 LYS PHE THR CYS ASP ARG LEU GLY ASP ASN ASP ILE ARG SEQRES 11 A 190 LEU HIS TYR GLN SER LYS ARG PRO PHE ALA SER PHE ALA SEQRES 12 A 190 GLU GLY LEU LEU ASP GLY CYS ALA GLU TYR PHE LYS GLU SEQRES 13 A 190 ASP PHE THR ILE SER ARG THR PRO GLU THR GLN ASP SER SEQRES 14 A 190 GLU THR ASP VAL ILE PHE ASN ILE THR ARG ALA PRO ARG SEQRES 15 A 190 GLY ALA GLU ASN LEU TYR PHE GLN HET IWP A 501 37 HET HEM A 502 73 HET CMO A 503 2 HETNAM IWP 5-FLUORO-2-{1-[(2-FLUOROPHENYL)METHYL]-5-(1,2-OXAZOL-3- HETNAM 2 IWP YL)-1H-PYRAZOL-3-YL}PYRIMIDIN-4-OL HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CMO CARBON MONOXIDE HETSYN HEM HEME FORMUL 2 IWP C17 H11 F2 N5 O2 FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 CMO C O HELIX 1 AA1 MET A 2 PHE A 17 1 16 HELIX 2 AA2 GLY A 18 CYS A 29 1 12 HELIX 3 AA3 ASP A 44 SER A 59 1 16 HELIX 4 AA4 PRO A 62 GLU A 80 1 19 HELIX 5 AA5 HIS A 82 MET A 89 1 8 HELIX 6 AA6 ASP A 91 SER A 97 1 7 HELIX 7 AA7 PHE A 102 LEU A 110 1 9 HELIX 8 AA8 PHE A 139 LYS A 155 1 17 SHEET 1 AA1 4 LYS A 118 ARG A 123 0 SHEET 2 AA1 4 ASP A 128 SER A 135 -1 O ARG A 130 N ASP A 122 SHEET 3 AA1 4 THR A 171 ARG A 179 -1 O ILE A 177 N ILE A 129 SHEET 4 AA1 4 PHE A 158 ARG A 162 -1 N SER A 161 O ASN A 176 LINK NE2 HIS A 104 FE HEM A 502 1555 1555 2.25 SITE 1 AC1 3 ASP A 15 GLU A 16 LEU A 69 SITE 1 AC2 8 MET A 1 PHE A 75 LEU A 78 ILE A 99 SITE 2 AC2 8 HIS A 104 VAL A 107 TYR A 133 CMO A 503 SITE 1 AC3 2 LEU A 146 HEM A 502 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1