PDB Short entry for 1B5B HEADER ELECTRON TRANSPORT 06-APR-98 1B5B TITLE RAT FERROCYTOCHROME B5 B CONFORMATION, NMR, 1 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERROCYTOCHROME B5; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HEME AS PROSTHETIC GROUP, WITH H63 AND H39 AS AXIAL COMPND 6 LIGANDS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3C KEYWDS ELECTRON TRANSPORT EXPDTA SOLUTION NMR AUTHOR B.DANGI,S.SARMA,C.YAN,D.BANVILLE,R.D.GUILES REVDAT 4 08-AUG-18 1B5B 1 SOURCE REMARK REVDAT 3 29-NOV-17 1B5B 1 REMARK HELIX REVDAT 2 24-FEB-09 1B5B 1 VERSN REVDAT 1 17-JUN-98 1B5B 0 JRNL AUTH B.DANGI,S.SARMA,C.YAN,D.L.BANVILLE,R.D.GUILES JRNL TITL THE ORIGIN OF DIFFERENCES IN THE PHYSICAL PROPERTIES OF THE JRNL TITL 2 EQUILIBRIUM FORMS OF CYTOCHROME B5 REVEALED THROUGH JRNL TITL 3 HIGH-RESOLUTION NMR STRUCTURES AND BACKBONE DYNAMIC JRNL TITL 4 ANALYSES. JRNL REF BIOCHEMISTRY V. 37 8289 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9622481 JRNL DOI 10.1021/BI9801964 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : WUTHRICH (DIANA), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B5B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171487. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : [U-13C; U-15N] CYTOCHROME B5, REMARK 210 100 MM PHOSPHATE BUFFER, 0.5 MM REMARK 210 TSP, PH 7.0, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY; TOCSY; N15 3D REMARK 210 NOESY-HMQC; N15 3D TOCSY-HMQC; REMARK 210 3D HCCH-TOCSY; HNCO; CBCA(CO)NH; REMARK 210 HSQC; HCACO< HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DIANA 2.1, X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : CLOSEST TO THE AVERAGE REMARK 210 STRUCTURE, LOW TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE REPRESENTS THE A CONFORMATION OF THE RAT REMARK 210 FERROCYTOCHROME B5. IT IS THE STRUCTURE CLOSEST TO THE REMARK 210 AVERAGE AS ANALYZED BY X-PLOR. 200 STRUCTURES WERE REMARK 210 CALCULATED USING DIANA 2.1 AND ONE STRUCTURE WAS CHOSEN TO REMARK 210 REPRESENT THE FINAL RESULTS. THE STRUCTURE WAS DETERMINED USING 2D REMARK 210 AND 3D EXPERIMENTS REMARK 210 INCLUDING DISTANCE AND ANGULAR RESTRAINTS FROM HNHA. 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 O GLU A 44 H GLU A 48 1.49 REMARK 500 O TRP A 22 H GLY A 51 1.52 REMARK 500 O TYR A 7 H HIS A 80 1.58 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 A 3 -57.58 76.32 REMARK 500 VAL A 4 159.54 -43.86 REMARK 500 HIS A 27 46.27 35.67 REMARK 500 PRO A 40 23.97 -75.03 REMARK 500 HIS A 63 133.55 -39.58 REMARK 500 TYR A 74 48.19 -92.27 REMARK 500 HIS A 80 145.92 -38.95 REMARK 500 ALA A 88 -76.28 67.23 REMARK 500 LYS A 89 123.27 171.99 REMARK 500 SER A 91 105.24 55.37 REMARK 500 GLU A 92 169.10 68.04 REMARK 500 THR A 93 -49.14 -160.38 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 95 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 NE2 REMARK 620 2 HEM A 95 NA 86.6 REMARK 620 3 HEM A 95 NB 92.1 90.8 REMARK 620 4 HEM A 95 NC 94.0 179.1 89.8 REMARK 620 5 HEM A 95 ND 88.5 89.7 179.3 89.7 REMARK 620 6 HIS A 63 NE2 170.9 99.4 81.2 80.0 98.2 REMARK 620 N 1 2 3 4 5 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 95 DBREF 1B5B A 1 94 UNP P00173 CYB5_RAT 5 98 SEQRES 1 A 94 ASP LYS ASP VAL LYS TYR TYR THR LEU GLU GLU ILE GLN SEQRES 2 A 94 LYS HIS LYS ASP SER LYS SER THR TRP VAL ILE LEU HIS SEQRES 3 A 94 HIS LYS VAL TYR ASP LEU THR LYS PHE LEU GLU GLU HIS SEQRES 4 A 94 PRO GLY GLY GLU GLU VAL LEU ARG GLU GLN ALA GLY GLY SEQRES 5 A 94 ASP ALA THR GLU ASN PHE GLU ASP VAL GLY HIS SER THR SEQRES 6 A 94 ASP ALA ARG GLU LEU SER LYS THR TYR ILE ILE GLY GLU SEQRES 7 A 94 LEU HIS PRO ASP ASP ARG SER LYS ILE ALA LYS PRO SER SEQRES 8 A 94 GLU THR LEU HET HEM A 95 73 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 HELIX 1 I LEU A 9 ILE A 12 1 4 HELIX 2 II THR A 33 GLU A 38 1 6 HELIX 3 III GLU A 44 ARG A 47 1 4 HELIX 4 IV ASP A 53 ASP A 60 1 8 HELIX 5 V THR A 65 SER A 71 1 7 HELIX 6 VI PRO A 81 LYS A 86 5 6 SHEET 1 I 5 LYS A 5 TYR A 7 0 SHEET 2 I 5 TYR A 74 HIS A 80 1 N GLU A 78 O LYS A 5 SHEET 3 I 5 HIS A 27 LEU A 32 -1 O HIS A 27 N LEU A 79 SHEET 4 I 5 THR A 21 LEU A 25 -1 O THR A 21 N LEU A 32 SHEET 5 I 5 GLY A 51 ALA A 54 1 N GLY A 51 O TRP A 22 LINK FE HEM A 95 NE2 HIS A 39 1555 1555 1.92 LINK FE HEM A 95 NE2 HIS A 63 1555 1555 2.01 SITE 1 AC1 13 VAL A 23 PHE A 35 HIS A 39 PRO A 40 SITE 2 AC1 13 GLY A 41 VAL A 45 LEU A 46 ALA A 54 SITE 3 AC1 13 ASN A 57 VAL A 61 HIS A 63 SER A 64 SITE 4 AC1 13 SER A 71 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