10 20 30 40 50 60 70 80 1LMS - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 02-MAY-02 1LMS
TITLE STRUCTURAL MODEL FOR AN ALKALINE FORM OF FERRICYTOCHROME C
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C, ISO-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS ALKALINE TRANSITION; CYTOCHROME C; NMR STRUCTURE, ELECTRON KEYWDS 2 TRANSPORT
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR M.ASSFALG,I.BERTINI,A.DOLFI,P.TURANO,A.G.MAUK,F.I.ROSELL, AUTHOR 2 H.B.GRAY
REVDAT 2 24-FEB-09 1LMS 1 VERSN REVDAT 1 18-MAR-03 1LMS 0
JRNL AUTH M.ASSFALG,I.BERTINI,A.DOLFI,P.TURANO,A.G.MAUK, JRNL AUTH 2 F.I.ROSELL,H.B.GRAY JRNL TITL STRUCTURAL MODEL FOR AN ALKALINE FORM OF JRNL TITL 2 FERRICYTOCHROME C JRNL REF J.AM.CHEM.SOC. V. 125 2913 2003 JRNL REFN ISSN 0002-7863 JRNL PMID 12617658 JRNL DOI 10.1021/JA027180S
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 6.0 REMARK 3 AUTHORS : CASE AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1LMS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-02. REMARK 100 THE RCSB ID CODE IS RCSB016089.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 11.1 REMARK 210 IONIC STRENGTH : 50 MM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM PROTEIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, 3D_15N- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 1.5, CORMA REMARK 210 METHOD USED : SIMULATED ANNEALING IN REMARK 210 TORSION ANGLE SPACE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE COORDINATES OF RESIDUES -5 TO 8 ARE NOT INCLUDED, REMARK 210 ALTHOUGH PRESENT IN THE SEQUENCE, BECAUSE NO CONSTRAINTS WERE REMARK 210 AVAILABLE
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 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 RES C SSSEQI REMARK 465 THR A -4 REMARK 465 GLU A -3 REMARK 465 PHE A -2 REMARK 465 LYS A -1 REMARK 465 ALA A 0 REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 LYS A 4 REMARK 465 LYS A 5 REMARK 465 GLY A 6 REMARK 465 ALA A 7 REMARK 465 THR A 8
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 TYR A 74 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ILE A 75 CA - CB - CG2 ANGL. DEV. = 12.7 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 LYS A 11 -41.73 -26.14 REMARK 500 CYS A 14 51.22 -144.93 REMARK 500 VAL A 20 -34.83 -136.44 REMARK 500 LYS A 22 114.74 70.09 REMARK 500 LYS A 27 -86.44 27.05 REMARK 500 VAL A 28 -124.04 -101.15 REMARK 500 HIS A 33 -19.63 61.59 REMARK 500 SER A 40 -178.17 56.01 REMARK 500 GLU A 44 9.43 -63.79 REMARK 500 TYR A 48 7.72 -58.64 REMARK 500 THR A 49 10.70 -37.95 REMARK 500 ASP A 50 44.49 -178.98 REMARK 500 ALA A 51 -96.50 179.74 REMARK 500 ASP A 60 82.23 -176.57 REMARK 500 GLU A 61 -153.33 -169.81 REMARK 500 ASN A 62 -56.96 -149.03 REMARK 500 PRO A 71 71.51 -69.18 REMARK 500 ALA A 72 -40.14 -141.64 REMARK 500 TYR A 74 90.43 -169.05 REMARK 500 ALA A 79 -164.68 67.19 REMARK 500 MET A 80 -61.71 -172.55 REMARK 500 ALA A 81 29.12 -72.68 REMARK 500 LYS A 86 -43.92 -155.54 REMARK 500 GLU A 88 -100.24 35.77 REMARK 500 LYS A 89 38.38 -172.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 18 THR A 19 147.82 REMARK 500 GLU A 21 LYS A 22 139.75 REMARK 500 PRO A 25 HIS A 26 -142.13 REMARK 500 HIS A 26 LYS A 27 149.07 REMARK 500 LYS A 27 VAL A 28 -115.64 REMARK 500 TYR A 46 SER A 47 -121.93 REMARK 500 ASP A 60 GLU A 61 -143.14 REMARK 500 GLY A 77 THR A 78 -138.49 REMARK 500 ALA A 79 MET A 80 -129.26 REMARK 500 ALA A 81 PHE A 82 148.54 REMARK 500 PHE A 82 GLY A 83 118.74 REMARK 500 GLY A 84 LEU A 85 120.39 REMARK 500 LEU A 85 LYS A 86 -144.55 REMARK 500 LYS A 86 LYS A 87 -121.45 REMARK 500 LYS A 87 GLU A 88 149.94 REMARK 500 GLU A 88 LYS A 89 -138.91 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 ARG A 38 0.14 SIDE_CHAIN REMARK 500 TYR A 46 0.11 SIDE_CHAIN REMARK 500 PHE A 82 0.17 SIDE_CHAIN REMARK 500 ARG A 91 0.13 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 HEC A 118 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 LYS A 73 NZ 169.6 REMARK 620 N 1
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 118
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YIC RELATED DB: PDB REMARK 900 CONTAINS THE SOLUTION STRUCTURE OF THE NATIVE YEAST ISO-1- REMARK 900 FERRICYTOCHROME C
DBREF 1LMS A -4 103 UNP P00044 CYC1_YEAST 1 108
SEQADV 1LMS ALA A 72 UNP P00044 LYS 77 ENGINEERED SEQADV 1LMS ALA A 79 UNP P00044 LYS 84 ENGINEERED SEQADV 1LMS THR A 102 UNP P00044 CYS 107 ENGINEERED
SEQRES 1 A 108 THR GLU PHE LYS ALA GLY SER ALA LYS LYS GLY ALA THR SEQRES 2 A 108 LEU PHE LYS THR ARG CYS LEU GLN CYS HIS THR VAL GLU SEQRES 3 A 108 LYS GLY GLY PRO HIS LYS VAL GLY PRO ASN LEU HIS GLY SEQRES 4 A 108 ILE PHE GLY ARG HIS SER GLY GLN ALA GLU GLY TYR SER SEQRES 5 A 108 TYR THR ASP ALA ASN ILE LYS LYS ASN VAL LEU TRP ASP SEQRES 6 A 108 GLU ASN ASN MET SER GLU TYR LEU THR ASN PRO ALA LYS SEQRES 7 A 108 TYR ILE PRO GLY THR ALA MET ALA PHE GLY GLY LEU LYS SEQRES 8 A 108 LYS GLU LYS ASP ARG ASN ASP LEU ILE THR TYR LEU LYS SEQRES 9 A 108 LYS ALA THR GLU
HET HEC A 118 75
HETNAM HEC HEME C
FORMUL 2 HEC C34 H34 FE N4 O4
HELIX 1 1 LEU A 9 CYS A 14 1 6 HELIX 2 2 ALA A 51 ASN A 56 1 6 HELIX 3 3 ASN A 62 ASN A 70 1 9 HELIX 4 4 LYS A 89 GLU A 103 1 15
SHEET 1 A 2 ARG A 38 HIS A 39 0 SHEET 2 A 2 LEU A 58 TRP A 59 -1 O TRP A 59 N ARG A 38
LINK NE2 HIS A 18 FE HEC A 118 1555 1555 1.96 LINK SG CYS A 14 CAB HEC A 118 1555 1555 1.83 LINK SG CYS A 17 CAC HEC A 118 1555 1555 1.81 LINK NZ LYS A 73 FE HEC A 118 1555 1555 2.04
SITE 1 AC1 12 CYS A 14 GLN A 16 CYS A 17 HIS A 18 SITE 2 AC1 12 VAL A 28 LEU A 32 GLY A 41 TYR A 48 SITE 3 AC1 12 ASN A 52 TRP A 59 LYS A 73 PHE A 82
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