HEADER HYDROLASE 17-MAR-06 2CI4 TITLE CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I CRYSTAL TITLE 2 FORM II COMPND MOL_ID: 1; COMPND 2 MOLECULE: NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I, COMPND 5 DIMETHYLARGININASE 1, DDAHI, DDAH-1; COMPND 6 EC: 3.5.3.18 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: BRAIN KEYWDS NOS REGULATION, S-NITROSYLATION, ZINC, HYDROLASE, NO, MMA, ADMA, KEYWDS 2 ACETYLATION, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.FREY,O.BRAUN,C.BRIAND,M.VASAK,M.G.GRUTTER REVDAT 3 13-DEC-23 2CI4 1 REMARK REVDAT 2 24-FEB-09 2CI4 1 VERSN REVDAT 1 17-MAY-06 2CI4 0 JRNL AUTH D.FREY,O.BRAUN,C.BRIAND,M.VASAK,M.G.GRUTTER JRNL TITL STRUCTURE OF THE MAMMALIAN NOS REGULATOR DIMETHYLARGININE JRNL TITL 2 DIMETHYLAMINOHYDROLASE: A BASIS FOR THE DESIGN OF SPECIFIC JRNL TITL 3 INHIBITORS. JRNL REF STRUCTURE V. 14 901 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16698551 JRNL DOI 10.1016/J.STR.2006.03.006 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 888688.990 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 32655 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1622 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4890 REMARK 3 BIN R VALUE (WORKING SET) : 0.0245 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 258 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2108 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.56000 REMARK 3 B22 (A**2) : -0.59000 REMARK 3 B33 (A**2) : -1.97000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.38000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.09 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.240 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.540 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.660 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 41.24 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CI4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1290026452. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32693 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.450 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1H70 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CITRIC ACID/NAOH, 20-40% PEG REMARK 280 8000, 2 MM TCEP, PH 5.0, PH 5.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.50750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 1 REMARK 465 SER A 2 REMARK 465 LEU A 3 REMARK 465 GLY A 4 REMARK 465 HIS A 5 REMARK 465 PRO A 6 REMARK 465 ALA A 7 REMARK 465 LYS A 281 REMARK 465 VAL A 282 REMARK 465 ASP A 283 REMARK 465 SER A 284 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 GLU A 84 -119.47 60.83 REMARK 500 PHE A 157 70.46 -108.97 REMARK 500 VAL A 168 -90.47 -80.53 REMARK 500 ASP A 169 54.87 -102.01 REMARK 500 SER A 178 168.10 176.14 REMARK 500 ASN A 183 19.17 56.74 REMARK 500 LYS A 229 -19.83 -149.40 REMARK 500 ASN A 261 28.74 -159.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2C6Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I IN REMARK 900 COMPLEX WITH CITRULLINE REMARK 900 RELATED ID: 2CI1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I IN REMARK 900 COMPLEX WITH S- NITROSO-LHOMOCYSTEINE REMARK 900 RELATED ID: 2CI3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE REMARK 900 CRYSTAL FORM I REMARK 900 RELATED ID: 2CI5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I IN REMARK 900 COMPLEX WITH L- HOMOCYSTEINE REMARK 900 RELATED ID: 2CI6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I REMARK 900 BOUND WITH ZINC LOW PH REMARK 900 RELATED ID: 2CI7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I IN REMARK 900 COMPLEX WITH ZINC , HIGH PH DBREF 2CI4 A 1 284 UNP P56965 DDAH1_BOVIN 1 284 SEQRES 1 A 284 ALA SER LEU GLY HIS PRO ALA THR PHE GLY ARG ALA THR SEQRES 2 A 284 HIS VAL VAL VAL ARG ALA LEU PRO GLU SER LEU ALA GLN SEQRES 3 A 284 GLN ALA LEU ARG ARG THR LYS GLY ASP GLU VAL ASP PHE SEQRES 4 A 284 ALA ARG ALA GLU ARG GLN HIS GLN LEU TYR VAL GLY VAL SEQRES 5 A 284 LEU GLY SER LYS LEU GLY LEU GLN VAL VAL GLN LEU PRO SEQRES 6 A 284 ALA ASP GLU SER LEU PRO ASP CYS VAL PHE VAL GLU ASP SEQRES 7 A 284 VAL ALA VAL VAL CYS GLU GLU THR ALA LEU ILE THR ARG SEQRES 8 A 284 PRO GLY ALA PRO SER ARG ARG LYS GLU ALA ASP MET MET SEQRES 9 A 284 LYS GLU ALA LEU GLU LYS LEU GLN LEU ASN ILE VAL GLU SEQRES 10 A 284 MET LYS ASP GLU ASN ALA THR LEU ASP GLY GLY ASP VAL SEQRES 11 A 284 LEU PHE THR GLY ARG GLU PHE PHE VAL GLY LEU SER LYS SEQRES 12 A 284 ARG THR ASN GLN ARG GLY ALA GLU ILE LEU ALA ASP THR SEQRES 13 A 284 PHE LYS ASP TYR ALA VAL SER THR VAL PRO VAL VAL ASP SEQRES 14 A 284 ALA LEU HIS LEU LYS SER PHE CYS SER MET ALA GLY PRO SEQRES 15 A 284 ASN LEU ILE ALA ILE GLY SER SER GLU SER ALA GLN LYS SEQRES 16 A 284 ALA LEU LYS ILE MET GLN GLN MET SER ASP HIS ARG TYR SEQRES 17 A 284 ASP LYS LEU THR VAL PRO ASP ASP THR ALA ALA ASN CYS SEQRES 18 A 284 ILE TYR LEU ASN ILE PRO SER LYS GLY HIS VAL LEU LEU SEQRES 19 A 284 HIS ARG THR PRO GLU GLU TYR PRO GLU SER ALA LYS VAL SEQRES 20 A 284 TYR GLU LYS LEU LYS ASP HIS MET LEU ILE PRO VAL SER SEQRES 21 A 284 ASN SER GLU LEU GLU LYS VAL ASP GLY LEU LEU THR CYS SEQRES 22 A 284 SER SER VAL LEU ILE ASN LYS LYS VAL ASP SER FORMUL 2 HOH *206(H2 O) HELIX 1 1 GLU A 22 LEU A 29 1 8 HELIX 2 2 ASP A 38 SER A 55 1 18 HELIX 3 3 PHE A 75 ASP A 78 5 4 HELIX 4 4 ALA A 94 LYS A 99 5 6 HELIX 5 5 GLU A 100 LEU A 111 1 12 HELIX 6 6 ASP A 126 GLY A 128 5 3 HELIX 7 7 ASN A 146 PHE A 157 1 12 HELIX 8 8 HIS A 172 SER A 175 5 4 HELIX 9 9 SER A 190 SER A 204 1 15 HELIX 10 10 ASP A 215 ASN A 220 5 6 HELIX 11 11 TYR A 241 GLU A 249 1 9 HELIX 12 12 GLU A 263 ASP A 268 5 6 HELIX 13 13 LEU A 270 SER A 275 5 6 SHEET 1 AA 3 GLN A 60 LEU A 64 0 SHEET 2 AA 3 HIS A 14 ARG A 18 1 O VAL A 15 N VAL A 62 SHEET 3 AA 3 VAL A 276 ILE A 278 -1 O VAL A 276 N VAL A 16 SHEET 1 AB 3 ALA A 80 CYS A 83 0 SHEET 2 AB 3 THR A 86 ILE A 89 -1 O THR A 86 N CYS A 83 SHEET 3 AB 3 ASN A 114 GLU A 117 1 O ASN A 114 N ALA A 87 SHEET 1 AC 3 VAL A 130 PHE A 132 0 SHEET 2 AC 3 GLU A 136 LEU A 141 -1 O PHE A 138 N LEU A 131 SHEET 3 AC 3 ALA A 161 PRO A 166 1 O ALA A 161 N PHE A 137 SHEET 1 AD 3 CYS A 177 GLY A 181 0 SHEET 2 AD 3 LEU A 184 ILE A 187 -1 O LEU A 184 N ALA A 180 SHEET 3 AD 3 ASP A 209 THR A 212 1 O ASP A 209 N ILE A 185 SHEET 1 AE 3 ILE A 222 ILE A 226 0 SHEET 2 AE 3 GLY A 230 ARG A 236 -1 O GLY A 230 N ILE A 226 SHEET 3 AE 3 HIS A 254 VAL A 259 1 O MET A 255 N LEU A 233 CRYST1 42.840 81.015 44.675 90.00 100.59 90.00 P 1 21 1 2 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 0.023343 0.000000 0.004364 0.00000 SCALE2 0.000000 0.012343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022772 0.00000