HEADER DE NOVO PROTEIN 08-AUG-06 2HZ8 TITLE QM/MM STRUCTURE REFINED FROM NMR-STRUCTURE OF A SINGLE CHAIN DIIRON TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED DIIRON PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FOUR-HELIX BUNDLE, DE NOVO PROTEIN EXPDTA SOLUTION NMR AUTHOR J.R.CALHOUN,W.LIU,K.SPIEGEL,M.DAL PERARO,M.L.KLEIN,A.J.WAND, AUTHOR 2 W.F.DEGRADO REVDAT 3 09-MAR-22 2HZ8 1 REMARK LINK REVDAT 2 11-MAR-08 2HZ8 1 JRNL VERSN REVDAT 1 17-JUL-07 2HZ8 0 JRNL AUTH J.R.CALHOUN,W.LIU,K.SPIEGEL,M.DAL PERARO,M.L.KLEIN, JRNL AUTH 2 K.G.VALENTINE,A.J.WAND,W.F.DEGRADO JRNL TITL SOLUTION NMR STRUCTURE OF A DESIGNED METALLOPROTEIN AND JRNL TITL 2 COMPLEMENTARY MOLECULAR DYNAMICS REFINEMENT. JRNL REF STRUCTURE V. 16 210 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18275812 JRNL DOI 10.1016/J.STR.2007.11.011 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.R.CALHOUN,H.KONO,S.LAHR,W.WANG,W.F.DEGRADO,J.G.SAVEN REMARK 1 TITL COMPUTATIONAL DESIGN AND CHARACTERIZATION OF A MONOMERIC REMARK 1 TITL 2 HELICAL DINUCLEAR METALLOPROTEIN. REMARK 1 REF J.MOL.BIOL. V. 334 1101 2003 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 14643669 REMARK 1 DOI 10.1016/J.JMB.2003.10.004 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.R.CALHOUN,F.NASTRI,O.MAGLOI,V.PAVONE,A.LOMBARDI, REMARK 1 AUTH 2 W.F.DEGRADO REMARK 1 TITL ARTIFICIAL DIIRON PROTEINS: FROM STRUCTURE TO FUNCTION. REMARK 1 REF BIOPOLYMERS V. 80 264 2005 REMARK 1 REFN ISSN 0006-3525 REMARK 1 PMID 15700297 REMARK 1 DOI 10.1002/BIP.20230 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, NAMD VERSION 2.6, AMBER VERSION 8, QM/MM REMARK 3 (VERSION 3.10), BASED ON CPMD AND GROMOS REMARK 3 AUTHORS : A. BRUNGER, P. ADAMS, M. CLORE, P.GROS, M. NILGES, REMARK 3 AND R. REED (CNS), LAXMIKANT, K, SKEEL, R, REMARK 3 BHANDARKAR, M, BRUNNER, R, GURSOY, A, KRAWETZ, N, REMARK 3 PHILLIPS, J, SHINOZAKI, A, VARADARAJAN, K,SCHULTEN, REMARK 3 K (NAMD), CASE, D. A., CHEATHAM, T. E., 3RD, REMARK 3 DARDEN, T., GOHLKE, H., LUO, R., MERZ, K. M., JR., REMARK 3 ONUFRIEV, A., SIMMERLING, C., WANG, B., WOODS, R. REMARK 3 J. (AMBER), CPMD: HUTTER, J, ALAVI, A, DEUTSCH, T, REMARK 3 BALLONE, P, BERNASCONI, M, FOCHER, P, GOEDECKER, S; REMARK 3 GROMOS SCOTT WRP, HUHNENBERGER, PH, TIRONI, TG, REMARK 3 MARK, AE, BILLETER SR, FENNEN J, TORDA AE, HUBER T, REMARK 3 KRUGER P, VAN GUNSTEREN WF: LAIO, A., REMARK 3 VANDEVONDELE, J., ROTHLISBERGER, U. (QM/MM) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AVERAGE OVER LAST PS OF 5PS QM/MM REMARK 3 TRAJECTORY. TWO METAL-SITE WATER MOLECULES ARE INCLUDED IN THE REMARK 3 AVERAGE. OTHER SOLVENT MOLECULES AND COUNTER IONS ARE EXCLUDED. REMARK 3 ATOMS INCLUDED IN THE QM-PART ARE INDICATED WITH A VALUE OF 1 IN REMARK 3 THE BETA-FACTOR COLUMN, WHEREAS ATOMS IN THE MM-PART ARE REMARK 3 INDICATED WITH A VALUE OF 0 IN THE BETA-FACTOR COLUMN. REMARK 4 REMARK 4 2HZ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000038937. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 10 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM DUE FERRI SINGLE CHAIN U REMARK 210 -15N, 13C, 2.5 MM ZN(II), 50 MM REMARK 210 DUETERATED SODIUM ACETATE 10 MM REMARK 210 NACL, 5% D2O; 2 MM DUE FERRI REMARK 210 SINGLE CHAIN U-15N, 10% 13C, 2.5 REMARK 210 MM ZN(II), 50 MM DUETERATED REMARK 210 SODIUM ACETATE 10 MM NACL, 5% REMARK 210 D2O; 2 MM DUE FERRI SINGLE CHAIN REMARK 210 U-15N, 13C, 2.5 MM ZN(II), 50 MM REMARK 210 DUETERATED SODIUM ACETATE 10 MM REMARK 210 NACL, 5% D2O REMARK 210 DIHEXANOYLPHOSPHATIDYLCHOLINE, REMARK 210 DIMYRISTOYLPHOSPHATIDYLCHOLINE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 4D_13C/15N- REMARK 210 SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY; HNHA; IPAP-15N REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE LINUX9, SPARKY 3.110, REMARK 210 VNMR 6.1B REMARK 210 METHOD USED : 1. STEP: CLASSICAL MOLECULAR REMARK 210 DYNAMICS SIMULATION STARTING REMARK 210 FROM NMR-STRUCTURE, USING NON- REMARK 210 BONDED MODEL FOR METAL-SITE. 2. REMARK 210 STEP: QM/MM MD FOR RELAXATION OF REMARK 210 LOCAL FRUSTRATIONS AT THE METAL REMARK 210 SITE. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : DYNAMICAL AVERAGE OF 300K REMARK 210 TRAJECTORY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS FIRST DETERMINED USING TRIPLE-RESONANCE REMARK 210 SPECTRSCOPY. THE STRUCTURE WAS THEN FURTHER REFINED USING REMARK 210 CLASSICAL MD FOLLOWED BY 5 PS OF CAR PARRINELLO HYBRID QM/MM REMARK 210 DYNAMICS. 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: 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 GLU A 72 CD GLU A 72 OE1 -0.072 REMARK 500 GLU A 72 CD GLU A 72 OE2 -0.073 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 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 106 NE - CZ - NH1 ANGL. DEV. = 3.5 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 ALA A 90 25.26 -140.13 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 ZN A 117 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 11 OE1 REMARK 620 2 GLU A 74 OE2 124.5 REMARK 620 3 GLU A 104 OE1 97.4 111.8 REMARK 620 4 HIS A 107 ND1 107.2 104.9 110.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 116 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 44 OE1 REMARK 620 2 GLU A 74 OE1 95.8 REMARK 620 3 HIS A 77 ND1 120.2 99.2 REMARK 620 4 GLU A 104 OE2 132.3 106.8 97.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 116 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 117 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U7J RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF FOUR HELIX-BUNDLE MODEL REMARK 900 RELATED ID: 1NVO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF FOUR HELIX-BUNDLE MODEL REMARK 900 RELATED ID: 1JMB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL REMARK 900 RELATED ID: 1JMO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL REMARK 900 RELATED ID: 1EC5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL REMARK 900 RELATED ID: 1MFT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL: DUE FERRI (II) TURN REMARK 900 MUTANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 NO SUITABLE DATABASE REFERENCES WERE REMARK 999 FOUND AT TIME OF PROCESSING DBREF 2HZ8 A 1 115 PDB 2HZ8 2HZ8 1 115 SEQRES 1 A 115 MET ASP GLU LEU ARG GLU LEU LEU LYS ALA GLU GLN GLN SEQRES 2 A 115 ALA ILE LYS ILE TYR LYS GLU VAL LEU LYS LYS ALA LYS SEQRES 3 A 115 GLU GLY ASP GLU GLN GLU LEU ALA ARG LEU ILE GLN GLU SEQRES 4 A 115 ILE VAL LYS ALA GLU LYS GLN ALA VAL LYS VAL TYR LYS SEQRES 5 A 115 GLU ALA ALA GLU LYS ALA ARG ASN PRO GLU LYS ARG GLN SEQRES 6 A 115 VAL ILE ASP LYS ILE LEU GLU ASP GLU GLU LYS HIS ILE SEQRES 7 A 115 GLU TRP LEU LYS ALA ALA SER LYS GLN GLY ASN ALA GLU SEQRES 8 A 115 GLN PHE ALA SER LEU VAL GLN GLN ILE LEU GLN ASP GLU SEQRES 9 A 115 GLN ARG HIS VAL GLU GLU ILE GLU LYS LYS ASN HET ZN A 116 1 HET ZN A 117 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *2(H2 O) HELIX 1 1 GLU A 3 GLY A 28 1 26 HELIX 2 2 ASP A 29 ALA A 34 1 6 HELIX 3 3 LEU A 36 LYS A 57 1 22 HELIX 4 4 VAL A 66 GLN A 87 1 22 HELIX 5 5 GLN A 92 ILE A 111 1 20 LINK OE1 GLU A 11 ZN ZN A 117 1555 1555 1.98 LINK OE1 GLU A 44 ZN ZN A 116 1555 1555 2.01 LINK OE1 GLU A 74 ZN ZN A 116 1555 1555 2.11 LINK OE2 GLU A 74 ZN ZN A 117 1555 1555 2.00 LINK ND1 HIS A 77 ZN ZN A 116 1555 1555 2.04 LINK OE2 GLU A 104 ZN ZN A 116 1555 1555 2.07 LINK OE1 GLU A 104 ZN ZN A 117 1555 1555 2.06 LINK ND1 HIS A 107 ZN ZN A 117 1555 1555 2.10 SITE 1 AC1 4 GLU A 44 GLU A 74 HIS A 77 GLU A 104 SITE 1 AC2 4 GLU A 11 GLU A 74 GLU A 104 HIS A 107 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