HEADER HEME-BINDING PROTEIN 06-AUG-08 2K78 TITLE SOLUTION STRUCTURE OF THE ISDC NEAT DOMAIN BOUND TO ZINC TITLE 2 PROTOPORPHYRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRON-REGULATED SURFACE DETERMINANT PROTEIN C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NEAT DOMAIN, UNP RESIDUES 25-150; COMPND 5 SYNONYM: STAPHYLOCOCCAL IRON-REGULATED PROTEIN D; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS (STRAIN MW2); SOURCE 3 ORGANISM_TAXID: 196620; SOURCE 4 GENE: ISDC, SIRD, MW1013; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS NEAT DOMAIN, NMR COMPLEX, HEME, ISD, ISDC, CELL WALL, IRON, METAL- KEYWDS 2 BINDING, PEPTIDOGLYCAN-ANCHOR, SECRETED, TRANSPORT PROTEIN, HEME- KEYWDS 3 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR V.A.VILLAREAL,R.M.PILPA,S.A.ROBSON,E.A.FADEEV,R.T.CLUBB REVDAT 6 22-MAY-24 2K78 1 REMARK REVDAT 5 16-MAR-22 2K78 1 REMARK SEQADV REVDAT 4 24-FEB-09 2K78 1 VERSN REVDAT 3 25-NOV-08 2K78 1 JRNL REVDAT 2 09-SEP-08 2K78 1 JRNL REVDAT 1 19-AUG-08 2K78 0 JRNL AUTH V.A.VILLAREAL,R.M.PILPA,S.A.ROBSON,E.A.FADEEV,R.T.CLUBB JRNL TITL THE ISDC PROTEIN FROM STAPHYLOCOCCUS AUREUS USES A FLEXIBLE JRNL TITL 2 BINDING POCKET TO CAPTURE HEME. JRNL REF J.BIOL.CHEM. V. 283 31591 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18715872 JRNL DOI 10.1074/JBC.M801126200 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: NULL REMARK 4 REMARK 4 2K78 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000100763. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 302 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 50 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 0.01 % SODIUM REMARK 210 AZIDE, 1.3 MM [U-100% 13C; U-100% REMARK 210 15N] ISDC, 2.1 MM REMARK 210 PROTOPORPHYRIN IX CONTAINING ZN, REMARK 210 7 % [U-100% 2H] D2O, 93% H2O/7% REMARK 210 D2O; 50 MM SODIUM PHOSPHATE, 100 REMARK 210 MM SODIUM CHLORIDE, 0.01 % REMARK 210 SODIUM AZIDE, 1.1 MM ISDC, 2.3 REMARK 210 MM PROTOPORPHYRIN IX CONTAINING REMARK 210 ZN, 100 % D2O, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNHA; 3D HCCH-COSY; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D HNCO; REMARK 210 3D HNHB REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP, NMRPIPE, ATNOS/CANDID, REMARK 210 CARA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-30 REMARK 465 RES C SSSEQI REMARK 465 MET A 4 REMARK 465 GLY A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 HIS A 13 REMARK 465 SER A 14 REMARK 465 SER A 15 REMARK 465 GLY A 16 REMARK 465 LEU A 17 REMARK 465 VAL A 18 REMARK 465 PRO A 19 REMARK 465 ARG A 20 REMARK 465 GLY A 21 REMARK 465 SER A 22 REMARK 465 HIS A 23 REMARK 465 MET A 24 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-30 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLY A 150 O 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 O SER A 82 H LYS A 116 1.60 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 ALA A 28 53.48 178.87 REMARK 500 1 ALA A 29 -150.74 -74.30 REMARK 500 1 ILE A 48 -70.91 -136.93 REMARK 500 1 TYR A 52 15.73 -142.91 REMARK 500 1 LYS A 62 62.21 -153.27 REMARK 500 1 ASN A 63 82.44 46.98 REMARK 500 1 TYR A 67 -153.70 -137.98 REMARK 500 1 VAL A 68 135.98 -170.73 REMARK 500 1 HIS A 74 99.85 55.04 REMARK 500 1 SER A 92 95.91 -167.22 REMARK 500 1 LYS A 108 -167.85 46.21 REMARK 500 1 LEU A 109 70.98 -150.25 REMARK 500 1 ASP A 122 95.79 -160.57 REMARK 500 1 ASP A 133 86.66 -168.01 REMARK 500 1 PRO A 145 -166.53 -58.57 REMARK 500 1 THR A 146 -54.01 -149.84 REMARK 500 1 ASP A 147 -76.71 -120.89 REMARK 500 1 ALA A 149 28.79 -157.98 REMARK 500 2 ILE A 48 -65.59 -137.25 REMARK 500 2 LYS A 62 62.04 -156.73 REMARK 500 2 ASN A 63 85.27 47.53 REMARK 500 2 TYR A 67 -155.46 -139.48 REMARK 500 2 VAL A 68 134.51 -170.67 REMARK 500 2 HIS A 74 99.30 58.42 REMARK 500 2 SER A 92 100.31 -167.04 REMARK 500 2 LYS A 108 -164.34 44.83 REMARK 500 2 LEU A 109 68.22 -150.64 REMARK 500 2 ASP A 133 87.40 -175.83 REMARK 500 2 ASP A 147 -43.12 -175.40 REMARK 500 3 ALA A 28 41.44 -143.81 REMARK 500 3 ALA A 29 -160.16 -165.55 REMARK 500 3 ASN A 42 -1.17 73.09 REMARK 500 3 ILE A 48 -64.94 -136.62 REMARK 500 3 LYS A 62 62.21 -159.03 REMARK 500 3 ASN A 63 84.00 48.97 REMARK 500 3 VAL A 68 135.98 -170.47 REMARK 500 3 HIS A 74 88.81 52.58 REMARK 500 3 SER A 92 100.40 -167.24 REMARK 500 3 ARG A 100 160.06 175.22 REMARK 500 3 LYS A 108 -166.04 47.41 REMARK 500 3 LEU A 109 62.75 -151.00 REMARK 500 3 GLU A 123 -164.73 -174.50 REMARK 500 3 ASP A 133 83.58 -170.45 REMARK 500 3 PRO A 145 -174.01 -63.22 REMARK 500 3 THR A 146 -42.74 -149.47 REMARK 500 3 ASP A 147 -49.16 -142.82 REMARK 500 3 ALA A 149 24.67 -158.55 REMARK 500 4 ALA A 29 -165.62 -165.74 REMARK 500 4 ILE A 48 -71.17 -137.32 REMARK 500 4 LYS A 62 62.25 -110.25 REMARK 500 REMARK 500 THIS ENTRY HAS 461 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZNH A 151 DBREF 2K78 A 25 150 UNP Q7A151 ISDC_STAAW 25 150 SEQADV 2K78 MET A 4 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 GLY A 5 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 SER A 6 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 SER A 7 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 HIS A 8 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 HIS A 9 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 HIS A 10 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 HIS A 11 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 HIS A 12 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 HIS A 13 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 SER A 14 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 SER A 15 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 GLY A 16 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 LEU A 17 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 VAL A 18 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 PRO A 19 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 ARG A 20 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 GLY A 21 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 SER A 22 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 HIS A 23 UNP Q7A151 EXPRESSION TAG SEQADV 2K78 MET A 24 UNP Q7A151 EXPRESSION TAG SEQRES 1 A 147 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 147 LEU VAL PRO ARG GLY SER HIS MET SER ALA ASN ALA ALA SEQRES 3 A 147 ASP SER GLY THR LEU ASN TYR GLU VAL TYR LYS TYR ASN SEQRES 4 A 147 THR ASN ASP THR SER ILE ALA ASN ASP TYR PHE ASN LYS SEQRES 5 A 147 PRO ALA LYS TYR ILE LYS LYS ASN GLY LYS LEU TYR VAL SEQRES 6 A 147 GLN ILE THR VAL ASN HIS SER HIS TRP ILE THR GLY MET SEQRES 7 A 147 SER ILE GLU GLY HIS LYS GLU ASN ILE ILE SER LYS ASN SEQRES 8 A 147 THR ALA LYS ASP GLU ARG THR SER GLU PHE GLU VAL SER SEQRES 9 A 147 LYS LEU ASN GLY LYS ILE ASP GLY LYS ILE ASP VAL TYR SEQRES 10 A 147 ILE ASP GLU LYS VAL ASN GLY LYS PRO PHE LYS TYR ASP SEQRES 11 A 147 HIS HIS TYR ASN ILE THR TYR LYS PHE ASN GLY PRO THR SEQRES 12 A 147 ASP VAL ALA GLY HET ZNH A 151 73 HETNAM ZNH PROTOPORPHYRIN IX CONTAINING ZN FORMUL 2 ZNH C34 H32 N4 O4 ZN HELIX 1 1 ILE A 48 TYR A 52 5 5 SHEET 1 A 9 HIS A 86 LYS A 87 0 SHEET 2 A 9 ILE A 78 ILE A 83 -1 N ILE A 83 O HIS A 86 SHEET 3 A 9 ILE A 113 LYS A 124 -1 O LYS A 116 N SER A 82 SHEET 4 A 9 PRO A 129 ASN A 143 -1 O TYR A 132 N ILE A 121 SHEET 5 A 9 SER A 31 LYS A 40 -1 N GLU A 37 O LYS A 141 SHEET 6 A 9 ALA A 57 LYS A 61 -1 O TYR A 59 N GLY A 32 SHEET 7 A 9 LEU A 66 ASN A 73 -1 O GLN A 69 N LYS A 58 SHEET 8 A 9 GLU A 99 GLU A 105 -1 O ARG A 100 N VAL A 72 SHEET 9 A 9 ASN A 89 ILE A 90 -1 O ASN A 89 N GLU A 103 CISPEP 1 LYS A 55 PRO A 56 1 -0.37 CISPEP 2 LYS A 55 PRO A 56 2 -0.29 CISPEP 3 LYS A 55 PRO A 56 3 -0.33 CISPEP 4 LYS A 55 PRO A 56 4 -0.23 CISPEP 5 LYS A 55 PRO A 56 5 -0.37 CISPEP 6 LYS A 55 PRO A 56 6 0.01 CISPEP 7 LYS A 55 PRO A 56 7 -0.08 CISPEP 8 LYS A 55 PRO A 56 8 -0.26 CISPEP 9 LYS A 55 PRO A 56 9 -0.19 CISPEP 10 LYS A 55 PRO A 56 10 -0.16 CISPEP 11 LYS A 55 PRO A 56 11 -0.13 CISPEP 12 LYS A 55 PRO A 56 12 -0.45 CISPEP 13 LYS A 55 PRO A 56 13 -0.24 CISPEP 14 LYS A 55 PRO A 56 14 -0.27 CISPEP 15 LYS A 55 PRO A 56 15 -0.39 CISPEP 16 LYS A 55 PRO A 56 16 -0.29 CISPEP 17 LYS A 55 PRO A 56 17 -0.50 CISPEP 18 LYS A 55 PRO A 56 18 -0.19 CISPEP 19 LYS A 55 PRO A 56 19 -0.41 CISPEP 20 LYS A 55 PRO A 56 20 -0.21 CISPEP 21 LYS A 55 PRO A 56 21 -0.03 CISPEP 22 LYS A 55 PRO A 56 22 -0.67 CISPEP 23 LYS A 55 PRO A 56 23 -0.37 CISPEP 24 LYS A 55 PRO A 56 24 -0.41 CISPEP 25 LYS A 55 PRO A 56 25 -0.20 CISPEP 26 LYS A 55 PRO A 56 26 -0.26 CISPEP 27 LYS A 55 PRO A 56 27 -0.15 CISPEP 28 LYS A 55 PRO A 56 28 -0.45 CISPEP 29 LYS A 55 PRO A 56 29 -0.49 CISPEP 30 LYS A 55 PRO A 56 30 -0.13 SITE 1 AC1 12 TYR A 39 LYS A 40 TYR A 41 ILE A 48 SITE 2 AC1 12 ALA A 49 TYR A 52 PHE A 53 HIS A 74 SITE 3 AC1 12 TRP A 77 ILE A 117 ILE A 121 TYR A 132 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