HEADER PROTEIN BINDING 09-APR-24 9BCH TITLE SOLUTION STRUCTURE OF THE HEMOGLOBIN RECEPTOR HBPA FROM TITLE 2 CORYNEBACTERIUM DIPHTHERIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEMBRANE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: A31S, TEV CLEAVAGE SCAR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE NCTC 13129; SOURCE 3 ORGANISM_TAXID: 257309; SOURCE 4 ATCC: 700971; SOURCE 5 GENE: DIP2330; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMAPLE4 KEYWDS RECEPTOR, CAPPING, BETA-SANDWICH, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.J.MAHONEY,R.T.CLUBB REVDAT 1 08-JAN-25 9BCH 0 JRNL AUTH B.J.MAHONEY,L.R.LYMAN,J.FORD,J.SOULE,N.A.CHEUNG,A.K.GORING, JRNL AUTH 2 K.ELLIS-GUARDIOLA,M.J.COLLAZO,D.CASCIO,H.TON-THAT, JRNL AUTH 3 M.P.SCHMITT,R.T.CLUBB JRNL TITL MOLECULAR BASIS OF HEMOGLOBIN BINDING AND HEME REMOVAL IN JRNL TITL 2 CORYNEBACTERIUM DIPHTHERIAE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 33122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 39739808 JRNL DOI 10.1073/PNAS.2411833122 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 3.6 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9BCH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-24. REMARK 100 THE DEPOSITION ID IS D_1000283058. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.72 MM [U-100% 13C; U-100% 15N] REMARK 210 HEMOGLOBIN RECEPTOR HBPA, 50 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 0.72 REMARK 210 MM [U-100% 13C; U-100% 15N] REMARK 210 HEMOGLOBIN RECEPTOR HBPA, 50 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HCCH-COSY; 3D HCCH-TOCSY; REMARK 210 3D H(CCO)NH; 3D 1H-15N TOCSY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-15N REMARK 210 NOESY; 3D HBHA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD; AVANCE NEO; REMARK 210 AVANCE DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.9.1.7, X-PLOR NIH 3.6, REMARK 210 XIPP 1.21.7, UNIO 10, TOPSPIN, REMARK 210 NMRPIPE 11.1, NMRFAM-SPARKY, REMARK 210 TALOS-N, PROCHECK / PROCHECK-NMR 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 THE LOWEST REMARK 210 ENERGY 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 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 1 PHE A 44 -53.96 74.84 REMARK 500 1 VAL A 85 157.47 -47.89 REMARK 500 1 LYS A 93 68.13 63.94 REMARK 500 1 LEU A 125 91.53 -68.82 REMARK 500 1 ASP A 129 -171.87 54.61 REMARK 500 1 ASN A 142 13.99 59.56 REMARK 500 1 THR A 183 43.96 -157.58 REMARK 500 1 THR A 184 -70.76 -162.97 REMARK 500 1 CYS A 211 44.81 -173.09 REMARK 500 1 LEU A 221 -49.74 -177.70 REMARK 500 2 PHE A 44 -61.22 74.42 REMARK 500 2 LYS A 61 43.13 72.91 REMARK 500 2 ARG A 91 152.91 -47.38 REMARK 500 2 PRO A 118 46.25 -86.28 REMARK 500 2 TYR A 127 23.01 179.95 REMARK 500 2 ASP A 129 -68.05 -142.86 REMARK 500 2 ASP A 135 59.61 70.19 REMARK 500 2 ASN A 142 13.62 55.91 REMARK 500 2 SER A 169 -164.79 -122.38 REMARK 500 2 ASP A 170 88.40 -69.68 REMARK 500 2 CYS A 182 159.23 -48.68 REMARK 500 2 THR A 183 72.36 179.89 REMARK 500 2 THR A 184 -76.04 -172.19 REMARK 500 2 HIS A 191 154.70 -49.39 REMARK 500 2 TYR A 209 48.64 -75.91 REMARK 500 2 CYS A 211 43.02 -170.08 REMARK 500 2 ASN A 212 167.71 -48.98 REMARK 500 2 PRO A 220 47.84 -81.93 REMARK 500 3 PHE A 44 -53.59 75.07 REMARK 500 3 HIS A 50 -94.78 -42.22 REMARK 500 3 TYR A 52 37.02 -95.81 REMARK 500 3 PRO A 57 -168.10 -68.94 REMARK 500 3 ARG A 91 155.98 -48.95 REMARK 500 3 LYS A 93 77.96 65.28 REMARK 500 3 ASN A 144 -62.85 -135.60 REMARK 500 3 ASN A 171 24.43 46.93 REMARK 500 3 PRO A 181 167.22 -46.58 REMARK 500 3 THR A 184 -80.26 -152.32 REMARK 500 3 PRO A 189 -82.33 -73.73 REMARK 500 3 LYS A 202 46.90 -87.79 REMARK 500 3 CYS A 211 77.11 -159.79 REMARK 500 3 LEU A 221 -56.48 -179.56 REMARK 500 4 PHE A 44 -53.66 75.47 REMARK 500 4 ARG A 91 165.50 -49.84 REMARK 500 4 LYS A 93 95.22 -160.82 REMARK 500 4 ASN A 142 11.61 59.27 REMARK 500 4 SER A 169 -166.34 -117.28 REMARK 500 4 THR A 183 31.75 172.63 REMARK 500 4 HIS A 191 156.96 -49.09 REMARK 500 4 LYS A 202 66.72 -103.95 REMARK 500 REMARK 500 THIS ENTRY HAS 254 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31164 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE HEMOGLOBIN RECEPTOR HBPA FROM REMARK 900 CORYNEBACTERIUM DIPHTHERIAE DBREF 9BCH A 32 229 UNP Q6NEE5 Q6NEE5_CORDI 32 229 SEQADV 9BCH SER A 32 UNP Q6NEE5 ALA 32 CONFLICT SEQRES 1 A 198 SER GLU GLU VAL LYS ASN ALA ASP LEU TYR TRP GLY PHE SEQRES 2 A 198 SER GLY SER SER HIS HIS LYS TYR ASP HIS ASN GLY PRO SEQRES 3 A 198 LYS PHE GLU LYS ALA GLY LYS GLY ALA GLU LEU THR ASN SEQRES 4 A 198 ILE ASP ALA ALA SER ALA TYR ALA GLU THR PHE LYS LYS SEQRES 5 A 198 GLY VAL PHE PRO ASN ASN LYS ARG GLU LYS SER ASP ILE SEQRES 6 A 198 LEU VAL PHE HIS ASN GLY GLU VAL LYS THR GLU THR ASN SEQRES 7 A 198 HIS SER SER TYR GLN ILE ASN TRP PRO GLY GLU VAL THR SEQRES 8 A 198 MET LYS LEU GLY TYR GLY ASP GLY LEU VAL ILE LYS ASP SEQRES 9 A 198 LEU ASN LEU MET LEU LYS ASN GLY ASN MET GLY GLU LEU SEQRES 10 A 198 LYS ALA THR VAL GLY GLU ASN SER ASN ILE THR LEU PHE SEQRES 11 A 198 ASP VAL GLN GLU TYR SER VAL SER ASP ASN THR ILE THR SEQRES 12 A 198 VAL THR PRO LYS ILE PRO PRO CYS THR THR GLY THR TRP SEQRES 13 A 198 LYS PRO TRP HIS ASN ASP LEU THR SER LYS LEU GLY SER SEQRES 14 A 198 LEU LYS SER VAL PHE PHE GLU SER TYR THR CYS ASN ASN SEQRES 15 A 198 ASP ASP ILE ALA LYS LYS PRO LEU PRO LEU THR VAL VAL SEQRES 16 A 198 LEU ASN GLY HELIX 1 AA1 ALA A 74 GLY A 84 1 11 HELIX 2 AA2 HIS A 191 LYS A 197 1 7 HELIX 3 AA3 LYS A 202 GLU A 207 1 6 HELIX 4 AA4 ASN A 212 LYS A 219 1 8 SHEET 1 AA1 6 LYS A 58 GLY A 63 0 SHEET 2 AA1 6 GLU A 120 LYS A 124 -1 O LYS A 124 N LYS A 58 SHEET 3 AA1 6 LEU A 131 LYS A 141 -1 O LEU A 131 N MET A 123 SHEET 4 AA1 6 TYR A 113 ASN A 116 -1 N ILE A 115 O LEU A 138 SHEET 5 AA1 6 ASP A 95 THR A 106 -1 N LYS A 105 O GLN A 114 SHEET 6 AA1 6 ALA A 66 ASN A 70 -1 N GLU A 67 O VAL A 98 SHEET 1 AA210 LYS A 58 GLY A 63 0 SHEET 2 AA210 GLU A 120 LYS A 124 -1 O LYS A 124 N LYS A 58 SHEET 3 AA210 LEU A 131 LYS A 141 -1 O LEU A 131 N MET A 123 SHEET 4 AA210 MET A 145 VAL A 152 -1 O THR A 151 N LYS A 134 SHEET 5 AA210 ASN A 155 VAL A 168 -1 O PHE A 161 N LEU A 148 SHEET 6 AA210 THR A 172 PRO A 177 -1 O THR A 174 N SER A 167 SHEET 7 AA210 LEU A 223 VAL A 226 -1 O LEU A 223 N VAL A 175 SHEET 8 AA210 ALA A 38 TRP A 42 -1 N TYR A 41 O THR A 224 SHEET 9 AA210 ASP A 95 THR A 106 -1 O PHE A 99 N LEU A 40 SHEET 10 AA210 ALA A 66 ASN A 70 -1 N GLU A 67 O VAL A 98 SSBOND 1 CYS A 182 CYS A 211 1555 1555 2.02 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