HEADER OXYGEN STORAGE/TRANSPORT 10-MAR-00 1EKY TITLE MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION CAVEAT 1EKY CHIRALITY ERRORS AT CA CENTERS OF ALA1 AND PRO53, 65 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C'; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER CAPSULATUS; SOURCE 3 ORGANISM_TAXID: 1061; SOURCE 4 STRAIN: M110 KEYWDS FOUR HELIX BUNDLE, OXYGEN STORAGE-TRANSPORT COMPLEX EXPDTA SOLUTION NMR NUMMDL 32 AUTHOR J.C.HUS,D.MARION,M.BLACKLEDGE REVDAT 4 16-FEB-22 1EKY 1 REMARK SEQADV REVDAT 3 24-FEB-09 1EKY 1 VERSN REVDAT 2 23-MAY-00 1EKY 1 JRNL REVDAT 1 17-MAR-00 1EKY 0 JRNL AUTH J.C.HUS,D.MARION,M.BLACKLEDGE JRNL TITL DE NOVO DETERMINATION OF PROTEIN STRUCTURE BY NMR USING JRNL TITL 2 ORIENTATIONAL AND LONG-RANGE ORDER RESTRAINTS. JRNL REF J.MOL.BIOL. V. 298 927 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10801359 JRNL DOI 10.1006/JMBI.2000.3714 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER MODIFIED VERSION OF DISCOVER, DISCOVER REMARK 3 MODIFIED VERSION OF DISCOVER REMARK 3 AUTHORS : HUS, MARION, BLACKLEDGE (DISCOVER), HUS, MARION, REMARK 3 BLACKLEDGE (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EKY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-00. REMARK 100 THE DEPOSITION ID IS D_1000010690. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 100MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 7MM CYT C', 15N, 100MM PO4 PH6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : IN-HOUSE MODIFICATION OF REMARK 210 DISCOVER CODE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 32 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 15 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 O ALA A 73 H TRP A 75 1.22 REMARK 500 O TYR A 125 H GLU A 127 1.32 REMARK 500 O ALA A 73 N TRP A 75 2.13 REMARK 500 O TYR A 125 N GLU A 127 2.18 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 5 PRO A 53 N - CA - CB ANGL. DEV. = 7.4 DEGREES REMARK 500 8 LEU A 47 N - CA - C ANGL. DEV. = -17.4 DEGREES REMARK 500 20 PRO A 53 N - CA - CB ANGL. DEV. = 7.7 DEGREES REMARK 500 31 PRO A 56 N - CA - CB ANGL. DEV. = 7.4 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 LYS A 29 -74.91 -75.54 REMARK 500 1 PHE A 31 -175.25 -69.07 REMARK 500 1 ASP A 32 -64.35 174.64 REMARK 500 1 ALA A 33 -49.83 168.96 REMARK 500 1 THR A 49 -71.38 -50.87 REMARK 500 1 ASP A 50 75.61 125.08 REMARK 500 1 PRO A 53 7.84 -174.48 REMARK 500 1 LEU A 54 -2.18 -147.90 REMARK 500 1 PRO A 56 -145.24 -159.26 REMARK 500 1 ALA A 57 77.79 -49.69 REMARK 500 1 SER A 60 79.92 69.06 REMARK 500 1 ASP A 63 -72.42 -54.75 REMARK 500 1 GLN A 67 -98.53 -65.35 REMARK 500 1 THR A 68 -152.81 42.28 REMARK 500 1 GLU A 69 -40.92 -153.74 REMARK 500 1 LYS A 71 -61.53 -157.09 REMARK 500 1 ALA A 73 -83.18 -56.43 REMARK 500 1 ILE A 74 -48.65 44.38 REMARK 500 1 TRP A 75 92.76 61.71 REMARK 500 1 ALA A 76 109.89 140.20 REMARK 500 1 ASN A 77 172.75 -54.84 REMARK 500 1 TYR A 125 47.67 -77.47 REMARK 500 1 ARG A 126 59.54 -56.05 REMARK 500 2 THR A 3 -68.92 175.92 REMARK 500 2 LYS A 4 60.28 -160.71 REMARK 500 2 LYS A 29 -76.33 -76.27 REMARK 500 2 PHE A 31 -176.24 -69.78 REMARK 500 2 ASP A 32 -64.54 174.43 REMARK 500 2 ALA A 33 -49.98 169.61 REMARK 500 2 LEU A 43 -70.25 -54.58 REMARK 500 2 ASP A 50 58.70 98.78 REMARK 500 2 ALA A 52 64.76 -59.08 REMARK 500 2 PRO A 53 -13.77 -174.85 REMARK 500 2 LEU A 54 -66.32 -98.63 REMARK 500 2 PRO A 56 -151.44 -73.11 REMARK 500 2 ALA A 57 90.61 -54.62 REMARK 500 2 THR A 59 -70.40 -158.71 REMARK 500 2 SER A 60 91.85 58.59 REMARK 500 2 THR A 62 159.21 175.47 REMARK 500 2 ASP A 63 -76.50 171.28 REMARK 500 2 LEU A 64 -55.27 -172.16 REMARK 500 2 GLN A 67 -150.20 -71.25 REMARK 500 2 GLU A 69 152.60 67.96 REMARK 500 2 ALA A 70 54.50 173.81 REMARK 500 2 LYS A 71 42.33 -67.52 REMARK 500 2 ALA A 73 13.48 43.73 REMARK 500 2 ILE A 74 -147.33 68.59 REMARK 500 2 TRP A 75 34.24 -146.88 REMARK 500 2 ALA A 76 20.70 49.38 REMARK 500 2 ALA A 101 -104.25 -64.09 REMARK 500 REMARK 500 THIS ENTRY HAS 861 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1 HEM A 130 REMARK 610 2 HEM A 130 REMARK 610 3 HEM A 130 REMARK 610 4 HEM A 130 REMARK 610 5 HEM A 130 REMARK 610 6 HEM A 130 REMARK 610 7 HEM A 130 REMARK 610 8 HEM A 130 REMARK 610 9 HEM A 130 REMARK 610 10 HEM A 130 REMARK 610 11 HEM A 130 REMARK 610 12 HEM A 130 REMARK 610 13 HEM A 130 REMARK 610 14 HEM A 130 REMARK 610 15 HEM A 130 REMARK 610 16 HEM A 130 REMARK 610 17 HEM A 130 REMARK 610 18 HEM A 130 REMARK 610 19 HEM A 130 REMARK 610 20 HEM A 130 REMARK 610 21 HEM A 130 REMARK 610 22 HEM A 130 REMARK 610 23 HEM A 130 REMARK 610 24 HEM A 130 REMARK 610 25 HEM A 130 REMARK 610 26 HEM A 130 REMARK 610 27 HEM A 130 REMARK 610 28 HEM A 130 REMARK 610 29 HEM A 130 REMARK 610 30 HEM A 130 REMARK 610 31 HEM A 130 REMARK 610 32 HEM A 130 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NBB RELATED DB: PDB REMARK 900 XRAY STRUCTURE FOR COMPARISON PURPOSES DBREF 1EKY A 1 129 UNP P00147 CYCP_RHOCA 1 129 SEQADV 1EKY GLY A 19 UNP P00147 LYS 19 VARIANT SEQADV 1EKY ALA A 30 UNP P00147 SER 30 VARIANT SEQADV 1EKY VAL A 38 UNP P00147 ALA 38 VARIANT SEQADV 1EKY LYS A 42 UNP P00147 ALA 42 VARIANT SEQADV 1EKY ALA A 76 UNP P00147 THR 76 VARIANT SEQADV 1EKY ASP A 79 UNP P00147 ALA 79 VARIANT SEQADV 1EKY HIS A 89 UNP P00147 ASN 89 VARIANT SEQADV 1EKY GLU A 90 UNP P00147 ASP 90 VARIANT SEQADV 1EKY GLY A 93 UNP P00147 ALA 93 VARIANT SEQADV 1EKY ALA A 94 UNP P00147 GLU 94 VARIANT SEQADV 1EKY GLY A 104 UNP P00147 ALA 104 VARIANT SEQADV 1EKY ALA A 105 UNP P00147 THR 105 VARIANT SEQRES 1 A 129 ALA ASP THR LYS GLU VAL LEU GLU ALA ARG GLU ALA TYR SEQRES 2 A 129 PHE LYS SER LEU GLY GLY SER MET LYS ALA MET THR GLY SEQRES 3 A 129 VAL ALA LYS ALA PHE ASP ALA GLU ALA ALA LYS VAL GLU SEQRES 4 A 129 ALA ALA LYS LEU GLU LYS ILE LEU ALA THR ASP VAL ALA SEQRES 5 A 129 PRO LEU PHE PRO ALA GLY THR SER SER THR ASP LEU PRO SEQRES 6 A 129 GLY GLN THR GLU ALA LYS ALA ALA ILE TRP ALA ASN MET SEQRES 7 A 129 ASP ASP PHE GLY ALA LYS GLY LYS ALA MET HIS GLU ALA SEQRES 8 A 129 GLY GLY ALA VAL ILE ALA ALA ALA ASN ALA GLY ASP GLY SEQRES 9 A 129 ALA ALA PHE GLY ALA ALA LEU GLN LYS LEU GLY GLY THR SEQRES 10 A 129 CYS LYS ALA CYS HIS ASP ASP TYR ARG GLU GLU ASP HET HEM A 130 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 HELIX 1 1 LYS A 4 ALA A 30 1 27 HELIX 2 2 ALA A 33 ALA A 48 1 16 HELIX 3 3 ASN A 77 GLY A 102 1 26 HELIX 4 4 ASP A 103 TYR A 125 1 23 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