PDB Short entry for 1N13 HEADER LYASE 16-OCT-02 1N13 TITLE THE CRYSTAL STRUCTURE OF PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE TITLE 2 FROM METHANOCOCCUS JANNASHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN; COMPND 3 CHAIN: A, C, E, G, I, K; COMPND 4 SYNONYM: PVLARGDC; COMPND 5 EC: 4.1.1.19; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN; COMPND 9 CHAIN: B, D, F, H, J, L; COMPND 10 SYNONYM: PVLARGDC; COMPND 11 EC: 4.1.1.19; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: MJ0316; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODON-PLUS(DE3)-RIL (STRATAGENE); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET19B (NOVAGEN); SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 12 ORGANISM_TAXID: 2190; SOURCE 13 GENE: MJ0316; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21-CODON-PLUS(DE3)-RIL (STRATAGENE); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET19B (NOVAGEN) KEYWDS PYRUVOYL GROUP, PYRUVATE, ARGININE DECARBOXYLASE, AGMATINE, ARGININE, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR W.D.TOLBERT,D.E.GRAHAM,R.H.WHITE,S.E.EALICK REVDAT 3 15-NOV-23 1N13 1 REMARK LINK ATOM REVDAT 2 24-FEB-09 1N13 1 VERSN REVDAT 1 25-MAR-03 1N13 0 JRNL AUTH W.D.TOLBERT,D.E.GRAHAM,R.H.WHITE,S.E.EALICK JRNL TITL PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE FROM METHANOCOCCUS JRNL TITL 2 JANNASCHII: CRYSTAL STRUCTURES OF THE SELF-CLEAVED AND S53A JRNL TITL 3 PROENZYME FORMS JRNL REF STRUCTURE V. 11 285 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12623016 JRNL DOI 10.1016/S0969-2126(03)00026-1 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.E.GRAHAM,H.XU,R.H.WHITE REMARK 1 TITL METHANOCOCCUS JANNASCHII USES A PYRUVOYL-DEPENDENT ARGININE REMARK 1 TITL 2 DECARBOXYLASE IN POLYAMINE BIOSYNTHESIS REMARK 1 REF J.BIOL.CHEM. V. 277 23500 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M203467200 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 57.9 REMARK 3 NUMBER OF REFLECTIONS : 101892 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) : 0.192 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 10235 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.002 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 5.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1507 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 181 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7174 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 118 REMARK 3 SOLVENT ATOMS : 736 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.81000 REMARK 3 B22 (A**2) : 6.79000 REMARK 3 B33 (A**2) : -2.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.99000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.11 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) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.160 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) : 1.440 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.130 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.180 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 34.16 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 : PROTEINAG2.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : MPD.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEINAG2.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : MPD.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 MODEL REFINED AGAINST FIRST CRYSTAL (CHESS) DATA REMARK 3 THEN LATER EXTENDED TO HIGHER RESOLUTION WITH INCLUSION REMARK 3 OF SECOND DATA SET (RFREE REFLECTIONS KEPT CONSISTENT WITH REMARK 3 ADDITION OF HIGHER RESOLUTION DATA). REMARK 4 REMARK 4 1N13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1000017387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-02; 01-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : CHESS; APS REMARK 200 BEAMLINE : F2; 8-BM REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980; 0.9793 REMARK 200 MONOCHROMATOR : SI 111; SI 111 REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 103325 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 59.9 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 4.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.10 REMARK 200 R MERGE FOR SHELL (I) : 0.22900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000, 2-METHYL-2,4-PENTANEDIOL, REMARK 280 GLYCEROL, N-[2-HYDROXYETHYL]PIPERAZINE-N'-[2-ETHANESULFONIC ACID] REMARK 280 , BETA-OCTYL GLUCOSIDE, PUTRESCINE, ETHYLENEDIAMINETETRAACETIC REMARK 280 ACID, DITHIOTHREITOL, ARGININE METHYL ESTER, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 46.44000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: TWO (ALPHA BETA)3 TRIMERS ARE IN THE ASYMMETRIC UNIT. 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -111.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, I, J, K, L 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 ALA A 3 REMARK 465 GLU A 4 REMARK 465 ILE A 5 REMARK 465 ASN A 6 REMARK 465 MET C 1 REMARK 465 ASN C 2 REMARK 465 ALA C 3 REMARK 465 GLU C 4 REMARK 465 MET E 1 REMARK 465 ASN E 2 REMARK 465 MET G 1 REMARK 465 ASN G 2 REMARK 465 ALA G 3 REMARK 465 GLU G 4 REMARK 465 ILE G 5 REMARK 465 ASN G 6 REMARK 465 PRO G 7 REMARK 465 LEU G 8 REMARK 465 HIS G 9 REMARK 465 ALA G 10 REMARK 465 TYR G 11 REMARK 465 MET I 1 REMARK 465 ASN I 2 REMARK 465 ALA I 3 REMARK 465 MET K 1 REMARK 465 ASN K 2 REMARK 465 ALA K 3 REMARK 465 GLU K 4 REMARK 465 ILE K 5 REMARK 465 ASN K 6 REMARK 465 PRO K 7 REMARK 465 LEU K 8 REMARK 465 HIS K 9 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 B 58 -4.05 71.08 REMARK 500 LYS B 152 -49.78 -132.39 REMARK 500 GLU D 58 -3.60 72.83 REMARK 500 LYS D 152 -51.14 -134.19 REMARK 500 LYS D 152 -51.04 -134.19 REMARK 500 TRP D 163 -156.29 -145.69 REMARK 500 LYS F 152 -44.47 -134.61 REMARK 500 GLU H 58 -1.01 68.99 REMARK 500 LYS H 152 -51.80 -130.77 REMARK 500 GLU J 58 -2.60 71.85 REMARK 500 LYS J 152 -49.93 -132.09 REMARK 500 GLU L 58 -7.52 72.45 REMARK 500 LYS L 152 -51.99 -137.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AG2 B 7011 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AG2 H 7012 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AG2 J 7013 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AG2 L 7014 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AG2 D 7015 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AG2 F 7016 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD D 7001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD L 7002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD H 7003 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD J 7004 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD F 7005 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD B 7006 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD H 7007 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD D 7008 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MT1 RELATED DB: PDB REMARK 900 METHANOCOCCUS JANNASCHII ARGININE DECARBOXYLASE ORIGINAL STRUCTURE REMARK 900 WITH SELENOMETHIONINE LABELED ENZYME REMARK 900 RELATED ID: 1N2M RELATED DB: PDB REMARK 900 S53A PROENZYME STRUCTURE DBREF 1N13 A 1 52 UNP Q57764 PDAD_METJA 1 52 DBREF 1N13 B 53 165 UNP Q57764 PDAD_METJA 54 165 DBREF 1N13 C 1 52 UNP Q57764 PDAD_METJA 1 52 DBREF 1N13 D 53 165 UNP Q57764 PDAD_METJA 54 165 DBREF 1N13 E 1 52 UNP Q57764 PDAD_METJA 1 52 DBREF 1N13 F 53 165 UNP Q57764 PDAD_METJA 54 165 DBREF 1N13 G 1 52 UNP Q57764 PDAD_METJA 1 52 DBREF 1N13 H 53 165 UNP Q57764 PDAD_METJA 54 165 DBREF 1N13 I 1 52 UNP Q57764 PDAD_METJA 1 52 DBREF 1N13 J 53 165 UNP Q57764 PDAD_METJA 54 165 DBREF 1N13 K 1 52 UNP Q57764 PDAD_METJA 1 52 DBREF 1N13 L 53 165 UNP Q57764 PDAD_METJA 54 165 SEQADV 1N13 PYR B 53 UNP Q57764 SER 53 SEE REMARK 999 SEQADV 1N13 PYR D 53 UNP Q57764 SER 53 SEE REMARK 999 SEQADV 1N13 PYR F 53 UNP Q57764 SER 53 SEE REMARK 999 SEQADV 1N13 PYR H 53 UNP Q57764 SER 53 SEE REMARK 999 SEQADV 1N13 PYR J 53 UNP Q57764 SER 53 SEE REMARK 999 SEQADV 1N13 PYR L 53 UNP Q57764 SER 53 SEE REMARK 999 SEQRES 1 A 52 MET ASN ALA GLU ILE ASN PRO LEU HIS ALA TYR PHE LYS SEQRES 2 A 52 LEU PRO ASN THR VAL SER LEU VAL ALA GLY SER SER GLU SEQRES 3 A 52 GLY GLU THR PRO LEU ASN ALA PHE ASP GLY ALA LEU LEU SEQRES 4 A 52 ASN ALA GLY ILE GLY ASN VAL ASN LEU ILE ARG ILE SER SEQRES 1 B 113 PYR ILE MET PRO PRO GLU ALA GLU ILE VAL PRO LEU PRO SEQRES 2 B 113 LYS LEU PRO MET GLY ALA LEU VAL PRO THR ALA TYR GLY SEQRES 3 B 113 TYR ILE ILE SER ASP VAL PRO GLY GLU THR ILE SER ALA SEQRES 4 B 113 ALA ILE SER VAL ALA ILE PRO LYS ASP LYS SER LEU CYS SEQRES 5 B 113 GLY LEU ILE MET GLU TYR GLU GLY LYS CYS SER LYS LYS SEQRES 6 B 113 GLU ALA GLU LYS THR VAL ARG GLU MET ALA LYS ILE GLY SEQRES 7 B 113 PHE GLU MET ARG GLY TRP GLU LEU ASP ARG ILE GLU SER SEQRES 8 B 113 ILE ALA VAL GLU HIS THR VAL GLU LYS LEU GLY CYS ALA SEQRES 9 B 113 PHE ALA ALA ALA ALA LEU TRP TYR LYS SEQRES 1 C 52 MET ASN ALA GLU ILE ASN PRO LEU HIS ALA TYR PHE LYS SEQRES 2 C 52 LEU PRO ASN THR VAL SER LEU VAL ALA GLY SER SER GLU SEQRES 3 C 52 GLY GLU THR PRO LEU ASN ALA PHE ASP GLY ALA LEU LEU SEQRES 4 C 52 ASN ALA GLY ILE GLY ASN VAL ASN LEU ILE ARG ILE SER SEQRES 1 D 113 PYR ILE MET PRO PRO GLU ALA GLU ILE VAL PRO LEU PRO SEQRES 2 D 113 LYS LEU PRO MET GLY ALA LEU VAL PRO THR ALA TYR GLY SEQRES 3 D 113 TYR ILE ILE SER ASP VAL PRO GLY GLU THR ILE SER ALA SEQRES 4 D 113 ALA ILE SER VAL ALA ILE PRO LYS ASP LYS SER LEU CYS SEQRES 5 D 113 GLY LEU ILE MET GLU TYR GLU GLY LYS CYS SER LYS LYS SEQRES 6 D 113 GLU ALA GLU LYS THR VAL ARG GLU MET ALA LYS ILE GLY SEQRES 7 D 113 PHE GLU MET ARG GLY TRP GLU LEU ASP ARG ILE GLU SER SEQRES 8 D 113 ILE ALA VAL GLU HIS THR VAL GLU LYS LEU GLY CYS ALA SEQRES 9 D 113 PHE ALA ALA ALA ALA LEU TRP TYR LYS SEQRES 1 E 52 MET ASN ALA GLU ILE ASN PRO LEU HIS ALA TYR PHE LYS SEQRES 2 E 52 LEU PRO ASN THR VAL SER LEU VAL ALA GLY SER SER GLU SEQRES 3 E 52 GLY GLU THR PRO LEU ASN ALA PHE ASP GLY ALA LEU LEU SEQRES 4 E 52 ASN ALA GLY ILE GLY ASN VAL ASN LEU ILE ARG ILE SER SEQRES 1 F 113 PYR ILE MET PRO PRO GLU ALA GLU ILE VAL PRO LEU PRO SEQRES 2 F 113 LYS LEU PRO MET GLY ALA LEU VAL PRO THR ALA TYR GLY SEQRES 3 F 113 TYR ILE ILE SER ASP VAL PRO GLY GLU THR ILE SER ALA SEQRES 4 F 113 ALA ILE SER VAL ALA ILE PRO LYS ASP LYS SER LEU CYS SEQRES 5 F 113 GLY LEU ILE MET GLU TYR GLU GLY LYS CYS SER LYS LYS SEQRES 6 F 113 GLU ALA GLU LYS THR VAL ARG GLU MET ALA LYS ILE GLY SEQRES 7 F 113 PHE GLU MET ARG GLY TRP GLU LEU ASP ARG ILE GLU SER SEQRES 8 F 113 ILE ALA VAL GLU HIS THR VAL GLU LYS LEU GLY CYS ALA SEQRES 9 F 113 PHE ALA ALA ALA ALA LEU TRP TYR LYS SEQRES 1 G 52 MET ASN ALA GLU ILE ASN PRO LEU HIS ALA TYR PHE LYS SEQRES 2 G 52 LEU PRO ASN THR VAL SER LEU VAL ALA GLY SER SER GLU SEQRES 3 G 52 GLY GLU THR PRO LEU ASN ALA PHE ASP GLY ALA LEU LEU SEQRES 4 G 52 ASN ALA GLY ILE GLY ASN VAL ASN LEU ILE ARG ILE SER SEQRES 1 H 113 PYR ILE MET PRO PRO GLU ALA GLU ILE VAL PRO LEU PRO SEQRES 2 H 113 LYS LEU PRO MET GLY ALA LEU VAL PRO THR ALA TYR GLY SEQRES 3 H 113 TYR ILE ILE SER ASP VAL PRO GLY GLU THR ILE SER ALA SEQRES 4 H 113 ALA ILE SER VAL ALA ILE PRO LYS ASP LYS SER LEU CYS SEQRES 5 H 113 GLY LEU ILE MET GLU TYR GLU GLY LYS CYS SER LYS LYS SEQRES 6 H 113 GLU ALA GLU LYS THR VAL ARG GLU MET ALA LYS ILE GLY SEQRES 7 H 113 PHE GLU MET ARG GLY TRP GLU LEU ASP ARG ILE GLU SER SEQRES 8 H 113 ILE ALA VAL GLU HIS THR VAL GLU LYS LEU GLY CYS ALA SEQRES 9 H 113 PHE ALA ALA ALA ALA LEU TRP TYR LYS SEQRES 1 I 52 MET ASN ALA GLU ILE ASN PRO LEU HIS ALA TYR PHE LYS SEQRES 2 I 52 LEU PRO ASN THR VAL SER LEU VAL ALA GLY SER SER GLU SEQRES 3 I 52 GLY GLU THR PRO LEU ASN ALA PHE ASP GLY ALA LEU LEU SEQRES 4 I 52 ASN ALA GLY ILE GLY ASN VAL ASN LEU ILE ARG ILE SER SEQRES 1 J 113 PYR ILE MET PRO PRO GLU ALA GLU ILE VAL PRO LEU PRO SEQRES 2 J 113 LYS LEU PRO MET GLY ALA LEU VAL PRO THR ALA TYR GLY SEQRES 3 J 113 TYR ILE ILE SER ASP VAL PRO GLY GLU THR ILE SER ALA SEQRES 4 J 113 ALA ILE SER VAL ALA ILE PRO LYS ASP LYS SER LEU CYS SEQRES 5 J 113 GLY LEU ILE MET GLU TYR GLU GLY LYS CYS SER LYS LYS SEQRES 6 J 113 GLU ALA GLU LYS THR VAL ARG GLU MET ALA LYS ILE GLY SEQRES 7 J 113 PHE GLU MET ARG GLY TRP GLU LEU ASP ARG ILE GLU SER SEQRES 8 J 113 ILE ALA VAL GLU HIS THR VAL GLU LYS LEU GLY CYS ALA SEQRES 9 J 113 PHE ALA ALA ALA ALA LEU TRP TYR LYS SEQRES 1 K 52 MET ASN ALA GLU ILE ASN PRO LEU HIS ALA TYR PHE LYS SEQRES 2 K 52 LEU PRO ASN THR VAL SER LEU VAL ALA GLY SER SER GLU SEQRES 3 K 52 GLY GLU THR PRO LEU ASN ALA PHE ASP GLY ALA LEU LEU SEQRES 4 K 52 ASN ALA GLY ILE GLY ASN VAL ASN LEU ILE ARG ILE SER SEQRES 1 L 113 PYR ILE MET PRO PRO GLU ALA GLU ILE VAL PRO LEU PRO SEQRES 2 L 113 LYS LEU PRO MET GLY ALA LEU VAL PRO THR ALA TYR GLY SEQRES 3 L 113 TYR ILE ILE SER ASP VAL PRO GLY GLU THR ILE SER ALA SEQRES 4 L 113 ALA ILE SER VAL ALA ILE PRO LYS ASP LYS SER LEU CYS SEQRES 5 L 113 GLY LEU ILE MET GLU TYR GLU GLY LYS CYS SER LYS LYS SEQRES 6 L 113 GLU ALA GLU LYS THR VAL ARG GLU MET ALA LYS ILE GLY SEQRES 7 L 113 PHE GLU MET ARG GLY TRP GLU LEU ASP ARG ILE GLU SER SEQRES 8 L 113 ILE ALA VAL GLU HIS THR VAL GLU LYS LEU GLY CYS ALA SEQRES 9 L 113 PHE ALA ALA ALA ALA LEU TRP TYR LYS HET PYR B 53 5 HET PYR D 53 5 HET PYR F 53 5 HET PYR H 53 5 HET PYR J 53 5 HET PYR L 53 5 HET AG2 B7011 9 HET MRD B7006 8 HET AG2 D7015 9 HET MRD D7001 8 HET MRD D7008 8 HET AG2 F7016 9 HET MRD F7005 8 HET AG2 H7012 9 HET MRD H7003 8 HET MRD H7007 8 HET AG2 J7013 9 HET MRD J7004 8 HET AG2 L7014 9 HET MRD L7002 8 HETNAM PYR PYRUVIC ACID HETNAM AG2 AGMATINE HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETSYN AG2 (4-AMINOBUTYL)GUANIDINE FORMUL 2 PYR 6(C3 H4 O3) FORMUL 13 AG2 6(C5 H14 N4) FORMUL 14 MRD 8(C6 H14 O2) FORMUL 27 HOH *736(H2 O) HELIX 1 1 THR A 29 GLY A 42 1 14 HELIX 2 2 SER B 115 GLY B 135 1 21 HELIX 3 3 HIS C 9 LYS C 13 5 5 HELIX 4 4 THR C 29 GLY C 42 1 14 HELIX 5 5 SER D 115 GLY D 135 1 21 HELIX 6 6 THR E 29 GLY E 42 1 14 HELIX 7 7 SER F 115 GLY F 135 1 21 HELIX 8 8 THR G 29 GLY G 42 1 14 HELIX 9 9 SER H 115 GLY H 135 1 21 HELIX 10 10 THR I 29 GLY I 42 1 14 HELIX 11 11 SER J 115 GLY J 135 1 21 HELIX 12 12 THR K 29 GLY K 42 1 14 HELIX 13 13 SER L 115 GLY L 135 1 21 SHEET 1 A 5 ASN A 47 ARG A 50 0 SHEET 2 A 5 LEU B 72 SER B 82 1 O VAL B 73 N ASN A 47 SHEET 3 A 5 GLY B 154 TRP B 163 -1 O ALA B 160 N ALA B 76 SHEET 4 A 5 THR A 17 GLU A 26 -1 N VAL A 21 O ALA B 159 SHEET 5 A 5 GLU B 60 ILE B 61 1 O GLU B 60 N VAL A 18 SHEET 1 B 3 LEU B 106 GLY B 112 0 SHEET 2 B 3 THR B 88 PRO B 98 -1 N ALA B 96 O LEU B 106 SHEET 3 B 3 LEU B 138 THR B 149 -1 O ASP B 139 N ILE B 97 SHEET 1 C 5 ASN C 47 ARG C 50 0 SHEET 2 C 5 LEU D 72 SER D 82 1 O VAL D 73 N ILE C 49 SHEET 3 C 5 GLY D 154 TRP D 163 -1 O ALA D 160 N ALA D 76 SHEET 4 C 5 THR C 17 GLU C 26 -1 N VAL C 21 O ALA D 159 SHEET 5 C 5 GLU D 60 ILE D 61 1 O GLU D 60 N VAL C 18 SHEET 1 D 3 LEU D 106 GLY D 112 0 SHEET 2 D 3 THR D 88 PRO D 98 -1 N ALA D 92 O TYR D 110 SHEET 3 D 3 LEU D 138 THR D 149 -1 O ASP D 139 N ILE D 97 SHEET 1 E 5 ASN E 47 ARG E 50 0 SHEET 2 E 5 LEU F 72 SER F 82 1 O VAL F 73 N ASN E 47 SHEET 3 E 5 GLY F 154 TRP F 163 -1 O ALA F 160 N ALA F 76 SHEET 4 E 5 THR E 17 GLU E 26 -1 N VAL E 21 O ALA F 159 SHEET 5 E 5 GLU F 60 ILE F 61 1 O GLU F 60 N VAL E 18 SHEET 1 F 3 LEU F 106 GLY F 112 0 SHEET 2 F 3 THR F 88 PRO F 98 -1 N ALA F 96 O LEU F 106 SHEET 3 F 3 LEU F 138 THR F 149 -1 O ASP F 139 N ILE F 97 SHEET 1 G 5 ASN G 47 ARG G 50 0 SHEET 2 G 5 LEU H 72 SER H 82 1 O VAL H 73 N ASN G 47 SHEET 3 G 5 GLY H 154 TRP H 163 -1 O ALA H 160 N ALA H 76 SHEET 4 G 5 THR G 17 GLU G 26 -1 N VAL G 21 O ALA H 159 SHEET 5 G 5 GLU H 60 ILE H 61 1 O GLU H 60 N VAL G 18 SHEET 1 H 3 LEU H 106 GLY H 112 0 SHEET 2 H 3 THR H 88 PRO H 98 -1 N ALA H 92 O TYR H 110 SHEET 3 H 3 LEU H 138 THR H 149 -1 O ARG H 140 N ILE H 97 SHEET 1 I 5 ASN I 47 ARG I 50 0 SHEET 2 I 5 LEU J 72 SER J 82 1 O VAL J 73 N ASN I 47 SHEET 3 I 5 GLY J 154 TRP J 163 -1 O ALA J 160 N ALA J 76 SHEET 4 I 5 THR I 17 GLU I 26 -1 N VAL I 21 O ALA J 159 SHEET 5 I 5 GLU J 60 ILE J 61 1 O GLU J 60 N VAL I 18 SHEET 1 J 3 LEU J 106 GLY J 112 0 SHEET 2 J 3 THR J 88 PRO J 98 -1 N ALA J 96 O LEU J 106 SHEET 3 J 3 LEU J 138 THR J 149 -1 O ARG J 140 N ILE J 97 SHEET 1 K 5 ASN K 47 ARG K 50 0 SHEET 2 K 5 LEU L 72 SER L 82 1 O THR L 75 N ILE K 49 SHEET 3 K 5 GLY L 154 TRP L 163 -1 O ALA L 160 N ALA L 76 SHEET 4 K 5 THR K 17 GLU K 26 -1 N VAL K 21 O ALA L 159 SHEET 5 K 5 GLU L 60 ILE L 61 1 O GLU L 60 N VAL K 18 SHEET 1 L 3 LEU L 106 GLY L 112 0 SHEET 2 L 3 THR L 88 PRO L 98 -1 N ALA L 96 O LEU L 106 SHEET 3 L 3 LEU L 138 THR L 149 -1 O ARG L 140 N ILE L 97 LINK C PYR B 53 N ILE B 54 1555 1555 1.33 LINK C PYR D 53 N ILE D 54 1555 1555 1.33 LINK C PYR F 53 N ILE F 54 1555 1555 1.33 LINK C PYR H 53 N ILE H 54 1555 1555 1.33 LINK C PYR J 53 N ILE J 54 1555 1555 1.33 LINK C PYR L 53 N ILE L 54 1555 1555 1.33 SITE 1 AC1 10 SER A 52 HOH A6663 PYR B 53 ILE B 107 SITE 2 AC1 10 GLU B 109 LEU C 31 ASP C 35 LEU C 38 SITE 3 AC1 10 GLY C 44 VAL C 46 SITE 1 AC2 10 SER G 52 HOH G6664 PYR H 53 ILE H 107 SITE 2 AC2 10 GLU H 109 LEU K 31 ASP K 35 LEU K 38 SITE 3 AC2 10 GLY K 44 VAL K 46 SITE 1 AC3 11 LEU G 31 ASP G 35 LEU G 38 GLY G 44 SITE 2 AC3 11 VAL G 46 HOH H6654 SER I 52 PYR J 53 SITE 3 AC3 11 ILE J 107 GLU J 109 HOH J6659 SITE 1 AC4 12 LEU I 31 ASP I 35 LEU I 38 GLY I 44 SITE 2 AC4 12 VAL I 46 HOH J6662 SER K 52 PYR L 53 SITE 3 AC4 12 ILE L 107 MET L 108 GLU L 109 HOH L6658 SITE 1 AC5 10 SER C 52 PYR D 53 ILE D 107 GLU D 109 SITE 2 AC5 10 HOH D6661 LEU E 31 ASP E 35 LEU E 38 SITE 3 AC5 10 GLY E 44 VAL E 46 SITE 1 AC6 10 PHE A 34 ASP A 35 LEU A 38 GLY A 44 SITE 2 AC6 10 VAL A 46 SER E 52 PYR F 53 ILE F 107 SITE 3 AC6 10 GLU F 109 HOH F6655 SITE 1 AC7 3 TYR D 77 TYR D 79 HOH D6656 SITE 1 AC8 5 HOH G6660 LEU K 31 TYR L 77 TYR L 79 SITE 2 AC8 5 ILE L 81 SITE 1 AC9 5 LEU G 31 PHE G 34 TYR H 77 TYR H 79 SITE 2 AC9 5 HOH H6654 SITE 1 BC1 5 LEU I 31 TYR J 77 TYR J 79 ILE J 81 SITE 2 BC1 5 HOH J6662 SITE 1 BC2 7 LEU E 31 PHE E 34 TYR F 77 TYR F 79 SITE 2 BC2 7 ILE F 81 HOH F6020 HOH F6673 SITE 1 BC3 6 LEU A 31 PHE A 34 TYR B 77 TYR B 79 SITE 2 BC3 6 ILE B 81 HOH B6653 SITE 1 BC4 7 GLU H 132 GLY H 135 TRP H 136 GLY L 135 SITE 2 BC4 7 TRP L 136 GLU L 137 HOH L6330 SITE 1 BC5 7 GLU D 132 GLY D 135 TRP D 136 GLY F 135 SITE 2 BC5 7 TRP F 136 HOH F6290 HOH F6320 CRYST1 56.460 92.880 87.110 90.00 94.74 90.00 P 1 21 1 12 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 0.017712 0.000000 0.001469 0.00000 SCALE2 0.000000 0.010767 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011519 0.00000