HEADER ELECTRON TRANSPORT 08-JAN-13 2M33 TITLE SOLUTION NMR STRUCTURE OF FULL-LENGTH OXIDIZED MICROSOMAL RABBIT TITLE 2 CYTOCHROME B5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME B5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-104; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 GENE: CYB5A, CYB5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSC KEYWDS MEMBRANE PROTEIN, HEME, HADDOCK, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 23 MDLTYP MINIMIZED AVERAGE AUTHOR V.SUBRAMANIAN,S.AHUJA,N.POPOVYCH,R.HUANG,S.V.LE CLAIR,N.JAHR,R.SOONG, AUTHOR 2 J.XU,K.YAMAMOTO,R.P.NANGA,S.IM,L.WASKELL,A.RAMAMOORTHY REVDAT 4 15-MAY-24 2M33 1 REMARK REVDAT 3 14-JUN-23 2M33 1 REMARK REVDAT 2 27-APR-16 2M33 1 ATOM DBREF REMARK SEQRES REVDAT 1 06-FEB-13 2M33 0 JRNL AUTH S.AHUJA,V.SUBRAMANIAN,N.POPOVYCH,R.HUANG,S.V.LE CLAIR, JRNL AUTH 2 N.JAHR,R.SOONG,J.XU,K.YAMAMOTO,R.P.NANGA,S.IM,L.WASKELL, JRNL AUTH 3 A.RAMAMOORTHY JRNL TITL NMR STRUCTURE OF FULL-LENGTH MAMMALIAN CYTOCHROME B5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, HADDOCK, CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 ALEXANDRE BONVIN (HADDOCK), GUNTERT, MUMENTHALER REMARK 3 AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M33 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000103147. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 45 MM [U-2H] DPC, 5 W/V REMARK 210 GLYCEROL, 100 MM POTASSIUM REMARK 210 PHOSPHATE, 0.001 MM DSS, 0.1-0.5 REMARK 210 MM [U-13C; U-15N] CYTOCHROME B5 REMARK 210 FULL-LENGTH, 0.1-0.5 MM HEME, 90% REMARK 210 H2O/10% D2O; 45 MM [U-2H] DPC, REMARK 210 5 W/V GLYCEROL, 100 MM POTASSIUM REMARK 210 PHOSPHATE, 0.001 MM DSS, 0.1-0.5 REMARK 210 MM [U-13C; U-15N; U-2H] REMARK 210 CYTOCHROME B5 FULL-LENGTH, 0.1- REMARK 210 0.5 MM HEME, 90% H2O/10% D2O; 45 REMARK 210 MM [U-2H] DPC, 5 W/V GLYCEROL, REMARK 210 100 MM POTASSIUM PHOSPHATE, REMARK 210 0.001 MM DSS, 0.1-0.5 MM REMARK 210 CYTOCHROME B5 FULL-LENGTH, 0.1- REMARK 210 0.5 MM HEME, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H NOESY; 3D HNCO; 3D HNCA; REMARK 210 3D HNCACB; 3D HN(CO)CA; 3D 1H- REMARK 210 15N NOESY; 3D 1H-15N TOCSY; 3D REMARK 210 1H-13C NOESY; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.113 REMARK 210 METHOD USED : DISTANCE GEOMETRY, TORSION ANGLE REMARK 210 DYNAMICS, SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 23 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 1-23 REMARK 465 RES C SSSEQI REMARK 465 SER A 105 REMARK 465 ASN A 106 REMARK 465 SER A 107 REMARK 465 SER A 108 REMARK 465 TRP A 109 REMARK 465 TRP A 110 REMARK 465 THR A 111 REMARK 465 ASN A 112 REMARK 465 TRP A 113 REMARK 465 VAL A 114 REMARK 465 ILE A 115 REMARK 465 PRO A 116 REMARK 465 ALA A 117 REMARK 465 ILE A 118 REMARK 465 SER A 119 REMARK 465 ALA A 120 REMARK 465 LEU A 121 REMARK 465 ILE A 122 REMARK 465 VAL A 123 REMARK 465 ALA A 124 REMARK 465 LEU A 125 REMARK 465 MET A 126 REMARK 465 TYR A 127 REMARK 465 ARG A 128 REMARK 465 LEU A 129 REMARK 465 TYR A 130 REMARK 465 MET A 131 REMARK 465 ALA A 132 REMARK 465 ASP A 133 REMARK 465 ASP A 134 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 OD1 ASP A 88 HZ2 LYS A 94 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 2 33.75 -145.06 REMARK 500 1 HIS A 22 -76.31 -112.68 REMARK 500 1 SER A 23 -50.80 -146.22 REMARK 500 1 SER A 25 27.83 -140.95 REMARK 500 1 LEU A 37 26.75 -142.28 REMARK 500 1 ARG A 89 -64.74 -124.97 REMARK 500 1 LYS A 91 -71.85 -156.54 REMARK 500 1 SER A 93 54.99 -101.63 REMARK 500 1 GLU A 97 92.49 59.59 REMARK 500 2 HIS A 22 -73.46 -114.60 REMARK 500 2 SER A 23 -48.59 -151.47 REMARK 500 2 SER A 25 29.65 -150.11 REMARK 500 2 LYS A 91 -62.22 -161.78 REMARK 500 2 SER A 93 70.93 -112.98 REMARK 500 2 GLU A 97 94.64 59.85 REMARK 500 3 ALA A 3 32.91 -144.20 REMARK 500 3 SER A 5 34.08 -146.62 REMARK 500 3 VAL A 9 75.19 -160.40 REMARK 500 3 HIS A 22 -66.96 -143.60 REMARK 500 3 SER A 23 -59.66 -152.48 REMARK 500 3 SER A 25 32.06 -150.43 REMARK 500 3 PRO A 45 42.22 -73.34 REMARK 500 3 ARG A 89 -70.96 -101.49 REMARK 500 3 SER A 90 68.93 -109.65 REMARK 500 3 LYS A 91 -72.59 -170.96 REMARK 500 3 MET A 96 -73.42 -124.98 REMARK 500 3 GLU A 97 102.17 65.37 REMARK 500 4 HIS A 22 -81.01 -105.13 REMARK 500 4 SER A 23 -76.31 -133.77 REMARK 500 4 LYS A 24 33.37 -88.74 REMARK 500 4 SER A 25 32.93 -151.49 REMARK 500 4 THR A 26 94.61 -69.27 REMARK 500 4 LYS A 91 -66.15 -140.15 REMARK 500 4 MET A 96 -66.85 -99.91 REMARK 500 4 GLU A 97 111.21 65.12 REMARK 500 5 HIS A 22 -75.06 -147.90 REMARK 500 5 SER A 23 -49.57 -148.56 REMARK 500 5 SER A 25 41.16 -154.72 REMARK 500 5 LEU A 37 27.22 -144.28 REMARK 500 5 LYS A 91 -60.18 -123.36 REMARK 500 5 MET A 96 -63.73 -129.52 REMARK 500 5 GLU A 97 104.88 62.80 REMARK 500 6 ALA A 2 56.69 -103.85 REMARK 500 6 SER A 25 41.59 -154.67 REMARK 500 6 PRO A 45 79.52 -69.22 REMARK 500 6 ARG A 89 -43.72 -132.25 REMARK 500 6 LYS A 91 -69.87 -169.97 REMARK 500 6 MET A 96 -67.99 -94.48 REMARK 500 6 GLU A 97 125.15 68.52 REMARK 500 7 SER A 25 41.63 -156.49 REMARK 500 REMARK 500 THIS ENTRY HAS 164 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 400 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 44 NE2 REMARK 620 2 HEM A 400 NA 89.0 REMARK 620 3 HEM A 400 NB 88.7 89.9 REMARK 620 4 HEM A 400 NC 88.9 177.9 89.8 REMARK 620 5 HEM A 400 ND 88.8 90.1 177.5 90.1 REMARK 620 6 HIS A 68 NE2 174.7 95.1 87.9 87.0 94.5 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 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18919 RELATED DB: BMRB DBREF 2M33 A 1 134 UNP P00169 CYB5_RABIT 1 134 SEQRES 1 A 134 MET ALA ALA GLN SER ASP LYS ASP VAL LYS TYR TYR THR SEQRES 2 A 134 LEU GLU GLU ILE LYS LYS HIS ASN HIS SER LYS SER THR SEQRES 3 A 134 TRP LEU ILE LEU HIS HIS LYS VAL TYR ASP LEU THR LYS SEQRES 4 A 134 PHE LEU GLU GLU HIS PRO GLY GLY GLU GLU VAL LEU ARG SEQRES 5 A 134 GLU GLN ALA GLY GLY ASP ALA THR GLU ASN PHE GLU ASP SEQRES 6 A 134 VAL GLY HIS SER THR ASP ALA ARG GLU LEU SER LYS THR SEQRES 7 A 134 PHE ILE ILE GLY GLU LEU HIS PRO ASP ASP ARG SER LYS SEQRES 8 A 134 LEU SER LYS PRO MET GLU THR LEU ILE THR THR VAL ASP SEQRES 9 A 134 SER ASN SER SER TRP TRP THR ASN TRP VAL ILE PRO ALA SEQRES 10 A 134 ILE SER ALA LEU ILE VAL ALA LEU MET TYR ARG LEU TYR SEQRES 11 A 134 MET ALA ASP ASP HET HEM A 400 73 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 HELIX 1 1 THR A 13 LYS A 18 1 6 HELIX 2 2 PHE A 40 HIS A 44 5 5 HELIX 3 3 GLU A 48 GLU A 53 1 6 HELIX 4 4 ALA A 59 GLY A 67 1 9 HELIX 5 5 SER A 69 SER A 76 1 8 HELIX 6 6 PRO A 86 ARG A 89 5 4 SHEET 1 A 4 LYS A 10 TYR A 12 0 SHEET 2 A 4 ILE A 80 LEU A 84 1 O GLU A 83 N TYR A 12 SHEET 3 A 4 LYS A 33 ASP A 36 -1 N VAL A 34 O GLY A 82 SHEET 4 A 4 TRP A 27 LEU A 30 -1 N LEU A 28 O TYR A 35 LINK NE2 HIS A 44 FE HEM A 400 1555 1555 2.23 LINK NE2 HIS A 68 FE HEM A 400 1555 1555 2.27 SITE 1 AC1 8 LEU A 30 LEU A 37 HIS A 44 PRO A 45 SITE 2 AC1 8 VAL A 50 VAL A 66 HIS A 68 SER A 69 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