HEADER ELECTRON TRANSPORT 27-MAR-01 1IB7 TITLE SOLUTION STRUCTURE OF F35Y MUTANT OF RAT FERRO CYTOCHROME B5, A TITLE 2 CONFORMATION, ENSEMBLE OF 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME B5; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS RATTUS; SOURCE 3 ORGANISM_COMMON: BLACK RAT; SOURCE 4 ORGANISM_TAXID: 10117; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3C KEYWDS CYTOCHROME B5, ELECTRON TRANSPORT, SOLUTION STRUCTURES EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.SHAHZAD,B.DANGI,J.I.BLANKMAN,R.D.GUILES REVDAT 3 27-OCT-21 1IB7 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1IB7 1 VERSN REVDAT 1 04-APR-01 1IB7 0 JRNL AUTH N.SHAHZAD,B.DANGI,J.I.BLANKMAN,R.D.GUILES JRNL TITL MUTAGENIC MODULATION OF THE ENTROPY CHANGE ON OXIDATION OF JRNL TITL 2 CYTOCHROME B5: AN ANALYSIS OF THE CONTRIBUTION OF JRNL TITL 3 CONFORMATIONAL ENTROPY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : GUENTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS CALCULATED USING 1167 REMARK 3 NOE RESTRAINTS AND 69 DIHEDRAL ANGLE RESTRAINTS; RESIDUES 1-3 REMARK 3 AND 89-94 WERE NOT INCLUDED IN THE REFINED MODEL BECAUSE OF A REMARK 3 LACK OF RESTRAINTS IN THESE PRESUMABLY UNSTRUCTURED REGIONS OF REMARK 3 THE PROTEIN. REMARK 4 REMARK 4 1IB7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAR-01. REMARK 100 THE DEPOSITION ID IS D_1000013120. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313; 313; 313 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 1MM; 1MM; 1MM REMARK 210 PRESSURE : NULL; NULL; NULL REMARK 210 SAMPLE CONTENTS : 2MM F35Y CYTOCHROME B5; 1MM REMARK 210 PHOSPHATE BUFFER; PURGED WITH REMARK 210 NITROGEN GAS AND REDUCED BY REMARK 210 ADDING FEW GRAINS OF SODIUM REMARK 210 DITHIONATE AND SEALED USING OXY- REMARK 210 ACETYLENE TORCH; 0.05 MM TSP AS REMARK 210 INTERNAL REFERENCE; 2MM F35Y REMARK 210 CYTOCHROME B5; 1MM PHOSPHATE REMARK 210 BUFFER; PURGED WITH NITROGEN GAS REMARK 210 AND REDUCED BY ADDING FEW GRAINS REMARK 210 OF SODIUM DITHIONATE AND SEALED REMARK 210 USING OXY-ACETYLENE TORCH; 0.05 REMARK 210 MM TSP AS INTERNAL REFERENCE; REMARK 210 2MM F35Y CYTOCHROME B5; 1MM REMARK 210 PHOSPHATE BUFFER; PURGED WITH REMARK 210 NITROGEN GAS AND REDUCED BY REMARK 210 ADDING FEW GRAINS OF SODIUM REMARK 210 DITHIONATE AND SEALED USING OXY- REMARK 210 ACETYLENE TORCH; 0.05 MM TSP AS REMARK 210 INTERNAL REFERENCE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; HNHA; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 97, XWINNMR 2.0 REMARK 210 METHOD USED : TORSION ANGEL DYNAMICS SIMULATED REMARK 210 ANNEALING; RESTRAINED ENERGY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY, TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 2D 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 TYR A 7 H HIS A 80 1.54 REMARK 500 O GLU A 56 H ASP A 60 1.56 REMARK 500 O LEU A 70 H TYR A 74 1.59 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 GLU A 11 -75.75 -61.64 REMARK 500 1 GLN A 13 -73.50 -55.00 REMARK 500 1 HIS A 15 45.88 -96.70 REMARK 500 1 HIS A 26 61.44 39.90 REMARK 500 1 LYS A 28 113.20 -169.96 REMARK 500 1 LEU A 32 39.66 -93.91 REMARK 500 1 ALA A 50 -92.11 -70.13 REMARK 500 1 HIS A 80 108.66 -38.68 REMARK 500 1 SER A 85 45.77 -90.85 REMARK 500 2 GLU A 11 -74.61 -61.61 REMARK 500 2 GLN A 13 -82.76 -61.80 REMARK 500 2 HIS A 15 48.31 -91.29 REMARK 500 2 HIS A 26 53.74 39.73 REMARK 500 2 LYS A 28 106.33 -169.95 REMARK 500 2 LEU A 32 36.29 -95.34 REMARK 500 2 ALA A 50 -90.11 -71.99 REMARK 500 2 THR A 55 -72.10 -50.43 REMARK 500 2 TYR A 74 41.61 -100.04 REMARK 500 2 HIS A 80 120.05 -38.52 REMARK 500 2 SER A 85 45.64 -109.37 REMARK 500 3 GLU A 11 -72.72 -61.71 REMARK 500 3 GLN A 13 -78.84 -59.40 REMARK 500 3 HIS A 15 43.67 -93.55 REMARK 500 3 HIS A 26 55.57 38.99 REMARK 500 3 LYS A 28 99.32 -168.91 REMARK 500 3 LEU A 32 44.95 -92.71 REMARK 500 3 GLU A 48 -36.43 -35.97 REMARK 500 3 GLN A 49 45.84 -143.24 REMARK 500 3 ALA A 50 -87.11 -65.48 REMARK 500 3 TYR A 74 37.94 -100.00 REMARK 500 3 HIS A 80 115.05 -37.84 REMARK 500 3 LYS A 86 30.76 -99.65 REMARK 500 4 GLU A 11 -73.53 -58.63 REMARK 500 4 GLN A 13 -78.97 -55.96 REMARK 500 4 HIS A 15 43.80 -94.13 REMARK 500 4 HIS A 26 60.31 38.83 REMARK 500 4 LYS A 28 107.07 -169.56 REMARK 500 4 LEU A 32 38.51 -90.81 REMARK 500 4 VAL A 45 -29.45 -39.86 REMARK 500 4 ALA A 50 -89.30 -68.50 REMARK 500 4 LYS A 86 35.36 -92.59 REMARK 500 5 GLU A 11 -75.66 -62.45 REMARK 500 5 GLN A 13 -70.42 -59.85 REMARK 500 5 HIS A 15 46.98 -89.76 REMARK 500 5 LYS A 28 106.20 -170.04 REMARK 500 5 LEU A 32 40.15 -92.54 REMARK 500 5 VAL A 45 -29.18 -39.98 REMARK 500 5 ALA A 50 -91.54 -70.74 REMARK 500 5 SER A 85 46.99 -93.18 REMARK 500 6 GLU A 11 -75.70 -60.09 REMARK 500 REMARK 500 THIS ENTRY HAS 184 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 95 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 NE2 REMARK 620 2 HEM A 95 NA 89.4 REMARK 620 3 HEM A 95 NB 96.9 90.8 REMARK 620 4 HEM A 95 NC 89.9 179.1 89.8 REMARK 620 5 HEM A 95 ND 82.7 89.7 179.3 89.7 REMARK 620 6 HIS A 63 NE2 172.9 97.7 83.5 83.0 96.9 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B5A RELATED DB: PDB REMARK 900 WILD TYPE FERRO CYTOCHROME B5, SOLUTION STRUCTURE DBREF 1IB7 A 1 94 UNP P00173 CYB5_RAT 5 98 SEQADV 1IB7 TYR A 35 UNP P00173 PHE 39 ENGINEERED MUTATION 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 TYR 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 1 THR A 8 HIS A 15 1 8 HELIX 2 2 GLU A 43 GLU A 48 1 6 HELIX 3 3 ALA A 54 ASP A 60 1 7 HELIX 4 4 SER A 64 TYR A 74 1 11 HELIX 5 5 HIS A 80 SER A 85 1 6 SHEET 1 A 3 TYR A 6 TYR A 7 0 SHEET 2 A 3 ILE A 75 LEU A 79 1 O GLU A 78 N TYR A 7 SHEET 3 A 3 VAL A 29 TYR A 30 -1 N VAL A 29 O GLY A 77 LINK NE2 HIS A 39 FE HEM A 95 1555 1555 2.10 LINK NE2 HIS A 63 FE HEM A 95 1555 1555 1.89 SITE 1 AC1 16 TYR A 30 LEU A 32 TYR A 35 HIS A 39 SITE 2 AC1 16 VAL A 45 LEU A 46 ALA A 54 PHE A 58 SITE 3 AC1 16 VAL A 61 GLY A 62 HIS A 63 SER A 64 SITE 4 AC1 16 ASP A 66 ALA A 67 LEU A 70 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 MODEL 1