PDB Short entry for 2I96 HEADER ELECTRON TRANSPORT 05-SEP-06 2I96 TITLE SOLUTION STRUCTURE OF THE OXIDIZED MICROSOMAL HUMAN CYTOCHROME B5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME B5; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS B5 FOLD, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.NUNEZ-QUINTANA,G.TRUAN,C.VAN HEIJENOORT REVDAT 3 09-MAR-22 2I96 1 REMARK REVDAT 2 24-FEB-09 2I96 1 VERSN REVDAT 1 04-SEP-07 2I96 0 JRNL AUTH M.NUNEZ-QUINTANA,G.TRUAN,C.VAN HEIJENOORT JRNL TITL SOLUTION STRUCTURE OF HUMAN CYTOCHROME B5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, CNS REMARK 3 AUTHORS : NILGES, M., LINGE, J.P. (ARIA), BRUNGER, A.T. ET REMARK 3 AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2I96 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039294. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM HUMAN CYTOCHROME B5 U-15N; REMARK 210 10MM PHOSPHATE BUFFER NA/K PH REMARK 210 6.5; 90% H2O, 10% D2O; 1MM HUMAN REMARK 210 CYTOCHROME B5 U-15N,13C; 10MM REMARK 210 PHOSPHATE BUFFER NA/K PH 6.5; D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AMX; ULTRA-SHIELD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 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 HG LEU A 112 H ASN A 113 1.25 REMARK 500 OE2 GLU A 94 HZ1 LYS A 97 1.58 REMARK 500 HZ2 LYS A 59 OE2 GLU A 62 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 12 TYR A 55 CE1 TYR A 55 CZ 0.092 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 8 PRO A 110 C - N - CA ANGL. DEV. = 10.5 DEGREES 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 22 -179.79 61.11 REMARK 500 1 GLU A 23 174.59 67.84 REMARK 500 1 SER A 25 -63.00 -144.02 REMARK 500 1 GLU A 27 -69.65 -150.66 REMARK 500 1 ALA A 28 -165.38 -118.94 REMARK 500 1 SER A 45 114.44 -171.60 REMARK 500 1 HIS A 51 -43.60 -162.21 REMARK 500 1 HIS A 52 -46.92 -149.35 REMARK 500 1 PRO A 65 109.92 -48.05 REMARK 500 1 GLU A 68 -82.34 52.74 REMARK 500 1 HIS A 88 -147.62 59.41 REMARK 500 1 PRO A 106 5.08 -50.21 REMARK 500 1 LYS A 111 -64.12 64.80 REMARK 500 1 LEU A 112 -88.19 -120.77 REMARK 500 1 LYS A 114 116.19 68.72 REMARK 500 1 THR A 118 162.75 71.12 REMARK 500 1 LEU A 119 -74.45 -58.44 REMARK 500 1 ILE A 120 -101.41 -127.12 REMARK 500 1 THR A 121 36.89 39.56 REMARK 500 1 SER A 125 -74.67 70.29 REMARK 500 1 SER A 126 -157.69 -113.62 REMARK 500 2 GLU A 23 -92.51 -100.81 REMARK 500 2 GLN A 24 -74.30 -161.27 REMARK 500 2 SER A 25 5.16 -152.04 REMARK 500 2 GLU A 27 -71.03 -57.48 REMARK 500 2 TYR A 32 -166.12 -127.55 REMARK 500 2 HIS A 51 62.84 66.80 REMARK 500 2 HIS A 52 -32.80 76.71 REMARK 500 2 THR A 58 -82.25 46.01 REMARK 500 2 PRO A 65 -72.11 -49.14 REMARK 500 2 GLU A 68 -85.11 58.18 REMARK 500 2 VAL A 70 33.63 -92.10 REMARK 500 2 ASP A 78 49.43 -76.90 REMARK 500 2 THR A 80 56.67 -68.23 REMARK 500 2 SER A 89 32.27 -81.68 REMARK 500 2 THR A 90 -42.36 70.59 REMARK 500 2 GLU A 94 -32.66 -132.21 REMARK 500 2 LYS A 111 -48.01 73.70 REMARK 500 2 LYS A 114 147.26 74.87 REMARK 500 2 LEU A 119 -100.46 -116.01 REMARK 500 2 ILE A 120 77.53 -118.03 REMARK 500 2 SER A 126 -74.12 -162.08 REMARK 500 3 GLN A 24 -68.40 68.62 REMARK 500 3 SER A 45 132.23 -179.21 REMARK 500 3 HIS A 52 -52.04 74.11 REMARK 500 3 ASP A 91 -57.25 -158.93 REMARK 500 3 LYS A 111 -75.51 64.32 REMARK 500 3 ASN A 113 -1.47 -159.39 REMARK 500 3 LYS A 114 71.04 61.25 REMARK 500 3 GLU A 117 -88.31 177.16 REMARK 500 REMARK 500 THIS ENTRY HAS 383 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 10 TYR A 55 0.06 SIDE CHAIN REMARK 500 12 TYR A 32 0.07 SIDE CHAIN REMARK 500 12 TYR A 55 0.07 SIDE CHAIN REMARK 500 19 TYR A 31 0.07 SIDE CHAIN 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 129 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 64 NE2 REMARK 620 2 HEM A 129 NA 91.3 REMARK 620 3 HEM A 129 NB 89.8 88.9 REMARK 620 4 HEM A 129 NC 90.2 177.9 89.5 REMARK 620 5 HEM A 129 ND 88.7 91.6 178.4 90.0 REMARK 620 6 HIS A 88 NE2 178.3 88.9 91.8 89.7 89.7 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HKO RELATED DB: PDB REMARK 900 OXIDIZED BOVIN CYTOCHROME B5 REMARK 900 RELATED ID: 1AW3 RELATED DB: PDB REMARK 900 OXIDIZED RAT CYTOCHROME B5 REMARK 900 RELATED ID: 1DO9 RELATED DB: PDB REMARK 900 OXIDIZED RABBIT CYTOCHROME B5 DBREF 2I96 A 21 128 UNP P00167 CYB5_HUMAN 0 107 SEQRES 1 A 108 MET ALA GLU GLN SER ASP GLU ALA VAL LYS TYR TYR THR SEQRES 2 A 108 LEU GLU GLU ILE GLN LYS HIS ASN HIS SER LYS SER THR SEQRES 3 A 108 TRP LEU ILE LEU HIS HIS LYS VAL TYR ASP LEU THR LYS SEQRES 4 A 108 PHE LEU GLU GLU HIS PRO GLY GLY GLU GLU VAL LEU ARG SEQRES 5 A 108 GLU GLN ALA GLY GLY ASP ALA THR GLU ASN PHE GLU ASP SEQRES 6 A 108 VAL GLY HIS SER THR ASP ALA ARG GLU MET SER LYS THR SEQRES 7 A 108 PHE ILE ILE GLY GLU LEU HIS PRO ASP ASP ARG PRO LYS SEQRES 8 A 108 LEU ASN LYS PRO PRO GLU THR LEU ILE THR THR ILE ASP SEQRES 9 A 108 SER SER SER SER HET HEM A 129 73 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 HELIX 1 1 THR A 33 GLN A 38 1 6 HELIX 2 2 GLU A 68 GLU A 73 1 6 HELIX 3 3 THR A 80 VAL A 86 1 7 HELIX 4 4 SER A 89 SER A 96 1 8 SHEET 1 A 5 TYR A 31 TYR A 32 0 SHEET 2 A 5 ILE A 100 LEU A 104 1 O GLU A 103 N TYR A 32 SHEET 3 A 5 LYS A 53 ASP A 56 -1 N VAL A 54 O GLY A 102 SHEET 4 A 5 SER A 45 ILE A 49 -1 N LEU A 48 O TYR A 55 SHEET 5 A 5 ASN A 41 HIS A 42 -1 N HIS A 42 O SER A 45 LINK NE2 HIS A 64 FE HEM A 129 1555 1555 2.01 LINK NE2 HIS A 88 FE HEM A 129 1555 1555 2.40 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