HEADER LYASE 19-DEC-01 1KNW TITLE CRYSTAL STRUCTURE OF DIAMINOPIMELATE DECARBOXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DAP DECARBOXYLASE; COMPND 5 EC: 4.1.1.20; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: LYSA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS PYRIDOXAL-PHOSPHATE, DECARBOXYLATION, DIAMINOPIMELATE, LYSINE, TIM- KEYWDS 2 BARREL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR V.LEVDIKOV,L.BLAGOVA,N.BOSE,C.MOMANY REVDAT 3 13-JUL-11 1KNW 1 VERSN REVDAT 2 24-FEB-09 1KNW 1 VERSN REVDAT 1 11-NOV-03 1KNW 0 JRNL AUTH V.LEVDIKOV,L.BLAGOVA,N.BOSE,C.MOMANY JRNL TITL DIAMINOPIMELATE DECARBOXYLASE USES A VERSATILE ACTIVE SITE JRNL TITL 2 FOR STEREOSPECIFIC DECARBOXYLATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 29454 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1495 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3264 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 393 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.010 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.012 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KNW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-02. REMARK 100 THE RCSB ID CODE IS RCSB015156. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 29807 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 10.200 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 27.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.20600 REMARK 200 R SYM FOR SHELL (I) : 0.20600 REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE, MES, PYRIDOXAL-5'- REMARK 280 PHOSPHATE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.98333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 117.96667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.47500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 147.45833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.49167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.98333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 117.96667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 147.45833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 88.47500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 29.49167 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 300 REMARK: THE ACTIVE BIOLOGICAL ENTITY IS A HOMODIMER. THE SECOND REMARK 300 MONOMER IS GENERATED FROM THE ASYMMETRYIC UNIT BY THE OPERATION: - REMARK 300 Y,-X,5/6-Z 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL 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 350 BIOMT1 2 0.500000 -0.866025 0.000000 49.29000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 85.37278 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 147.45833 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 HIS A 423 REMARK 465 HIS A 424 REMARK 465 HIS A 425 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 CYS A 56 101.89 -175.44 REMARK 500 ASN A 161 34.62 -99.42 REMARK 500 ILE A 192 -52.52 -122.52 REMARK 500 GLN A 234 125.07 -36.55 REMARK 500 THR A 349 78.56 -100.26 REMARK 500 HIS A 421 57.83 -174.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LEU A 392 -10.53 REMARK 500 HIS A 421 11.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG A 307 23.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 776 DISTANCE = 5.03 ANGSTROMS REMARK 525 HOH A 801 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 825 DISTANCE = 5.22 ANGSTROMS REMARK 525 HOH A 881 DISTANCE = 5.03 ANGSTROMS 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 LI A 530 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 645 O REMARK 620 2 LYS A 154 O 117.4 REMARK 620 3 HIS A 151 O 154.1 88.5 REMARK 620 4 SER A 152 O 89.4 105.2 82.5 REMARK 620 5 ASN A 156 OD1 87.6 107.7 84.9 144.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LI A 540 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 384 O REMARK 620 2 HOH A 590 O 115.0 REMARK 620 3 ASN A 303 ND2 69.2 86.3 REMARK 620 4 PRO A 390 O 161.9 80.3 104.0 REMARK 620 5 ARG A 389 O 89.6 150.3 87.5 73.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 520 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI A 530 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI A 540 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 554 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 510 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KO0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A D,L-LYSINE COMPLEX OF REMARK 900 DIAMINOPIMELATE DECARBOXYLASE DBREF 1KNW A 1 420 UNP P00861 DCDA_ECOLI 1 420 SEQADV 1KNW HIS A 421 UNP P00861 EXPRESSION TAG SEQADV 1KNW HIS A 422 UNP P00861 EXPRESSION TAG SEQADV 1KNW HIS A 423 UNP P00861 EXPRESSION TAG SEQADV 1KNW HIS A 424 UNP P00861 EXPRESSION TAG SEQADV 1KNW HIS A 425 UNP P00861 EXPRESSION TAG SEQRES 1 A 425 MET PRO HIS SER LEU PHE SER THR ASP THR ASP LEU THR SEQRES 2 A 425 ALA GLU ASN LEU LEU ARG LEU PRO ALA GLU PHE GLY CYS SEQRES 3 A 425 PRO VAL TRP VAL TYR ASP ALA GLN ILE ILE ARG ARG GLN SEQRES 4 A 425 ILE ALA ALA LEU LYS GLN PHE ASP VAL VAL ARG PHE ALA SEQRES 5 A 425 GLN LYS ALA CYS SER ASN ILE HIS ILE LEU ARG LEU MET SEQRES 6 A 425 ARG GLU GLN GLY VAL LYS VAL ASP SER VAL SER LEU GLY SEQRES 7 A 425 GLU ILE GLU ARG ALA LEU ALA ALA GLY TYR ASN PRO GLN SEQRES 8 A 425 THR HIS PRO ASP ASP ILE VAL PHE THR ALA ASP VAL ILE SEQRES 9 A 425 ASP GLN ALA THR LEU GLU ARG VAL SER GLU LEU GLN ILE SEQRES 10 A 425 PRO VAL ASN ALA GLY SER VAL ASP MET LEU ASP GLN LEU SEQRES 11 A 425 GLY GLN VAL SER PRO GLY HIS ARG VAL TRP LEU ARG VAL SEQRES 12 A 425 ASN PRO GLY PHE GLY HIS GLY HIS SER GLN LYS THR ASN SEQRES 13 A 425 THR GLY GLY GLU ASN SER LYS HIS GLY ILE TRP TYR THR SEQRES 14 A 425 ASP LEU PRO ALA ALA LEU ASP VAL ILE GLN ARG HIS HIS SEQRES 15 A 425 LEU GLN LEU VAL GLY ILE HIS MET HIS ILE GLY SER GLY SEQRES 16 A 425 VAL ASP TYR ALA HIS LEU GLU GLN VAL CYS GLY ALA MET SEQRES 17 A 425 VAL ARG GLN VAL ILE GLU PHE GLY GLN ASP LEU GLN ALA SEQRES 18 A 425 ILE SER ALA GLY GLY GLY LEU SER VAL PRO TYR GLN GLN SEQRES 19 A 425 GLY GLU GLU ALA VAL ASP THR GLU HIS TYR TYR GLY LEU SEQRES 20 A 425 TRP ASN ALA ALA ARG GLU GLN ILE ALA ARG HIS LEU GLY SEQRES 21 A 425 HIS PRO VAL LYS LEU GLU ILE GLU PRO GLY ARG PHE LEU SEQRES 22 A 425 VAL ALA GLN SER GLY VAL LEU ILE THR GLN VAL ARG SER SEQRES 23 A 425 VAL LYS GLN MET GLY SER ARG HIS PHE VAL LEU VAL ASP SEQRES 24 A 425 ALA GLY PHE ASN ASP LEU MET ARG PRO ALA MET TYR GLY SEQRES 25 A 425 SER TYR HIS HIS ILE SER ALA LEU ALA ALA ASP GLY ARG SEQRES 26 A 425 SER LEU GLU HIS ALA PRO THR VAL GLU THR VAL VAL ALA SEQRES 27 A 425 GLY PRO LEU CYS GLU SER GLY ASP VAL PHE THR GLN GLN SEQRES 28 A 425 GLU GLY GLY ASN VAL GLU THR ARG ALA LEU PRO GLU VAL SEQRES 29 A 425 LYS ALA GLY ASP TYR LEU VAL LEU HIS ASP THR GLY ALA SEQRES 30 A 425 TYR GLY ALA SER MET SER SER ASN TYR ASN SER ARG PRO SEQRES 31 A 425 LEU LEU PRO GLU VAL LEU PHE ASP ASN GLY GLN ALA ARG SEQRES 32 A 425 LEU ILE ARG ARG ARG GLN THR ILE GLU GLU LEU LEU ALA SEQRES 33 A 425 LEU GLU LEU LEU HIS HIS HIS HIS HIS HET SO4 A 520 5 HET LI A 530 1 HET LI A 540 1 HET PLP A 554 15 HET MES A 510 12 HETNAM SO4 SULFATE ION HETNAM LI LITHIUM ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 SO4 O4 S 2- FORMUL 3 LI 2(LI 1+) FORMUL 5 PLP C8 H10 N O6 P FORMUL 6 MES C6 H13 N O4 S FORMUL 7 HOH *393(H2 O) HELIX 1 1 THR A 13 GLY A 25 1 13 HELIX 2 2 ALA A 33 ALA A 42 1 10 HELIX 3 3 LYS A 54 CYS A 56 5 3 HELIX 4 4 ASN A 58 GLN A 68 1 11 HELIX 5 5 SER A 76 ALA A 86 1 11 HELIX 6 6 ASP A 105 GLN A 116 1 12 HELIX 7 7 SER A 123 SER A 134 1 12 HELIX 8 8 ASP A 170 HIS A 181 1 12 HELIX 9 9 ASP A 197 GLY A 216 1 20 HELIX 10 10 ASP A 240 GLY A 260 1 21 HELIX 11 11 GLY A 270 ALA A 275 1 6 HELIX 12 12 MET A 306 GLY A 312 1 7 HELIX 13 13 GLY A 379 SER A 383 5 5 HELIX 14 14 THR A 410 ALA A 416 1 7 SHEET 1 A11 GLN A 401 ARG A 406 0 SHEET 2 A11 GLU A 394 ASP A 398 -1 O GLU A 394 N ILE A 405 SHEET 3 A11 VAL A 28 ASP A 32 1 O TRP A 29 N VAL A 395 SHEET 4 A11 GLY A 278 MET A 290 -1 N VAL A 279 O VAL A 30 SHEET 5 A11 TYR A 369 LEU A 372 -1 N LEU A 370 O THR A 282 SHEET 6 A11 ILE A 317 LEU A 320 -1 O SER A 318 N VAL A 371 SHEET 7 A11 TYR A 369 LEU A 372 -1 O TYR A 369 N LEU A 320 SHEET 8 A11 GLY A 278 MET A 290 -1 O LEU A 280 N LEU A 372 SHEET 9 A11 ARG A 293 VAL A 298 -1 O ARG A 293 N MET A 290 SHEET 10 A11 THR A 332 ALA A 338 1 N VAL A 336 O HIS A 294 SHEET 11 A11 ARG A 359 PRO A 362 -1 O ARG A 359 N THR A 335 SHEET 1 B11 VAL A 48 ALA A 52 0 SHEET 2 B11 LYS A 71 SER A 74 1 O LYS A 71 N PHE A 51 SHEET 3 B11 ILE A 97 ALA A 101 1 O VAL A 98 N SER A 74 SHEET 4 B11 VAL A 119 ALA A 121 1 N ASN A 120 O PHE A 99 SHEET 5 B11 ARG A 138 ASN A 144 1 O ARG A 138 N VAL A 119 SHEET 6 B11 ILE A 166 TRP A 167 1 N ILE A 166 O ARG A 142 SHEET 7 B11 ARG A 138 ASN A 144 1 O ARG A 142 N ILE A 166 SHEET 8 B11 GLN A 184 HIS A 189 1 O GLN A 184 N VAL A 139 SHEET 9 B11 ALA A 221 SER A 223 1 N ALA A 221 O VAL A 186 SHEET 10 B11 LYS A 264 ILE A 267 1 O LYS A 264 N ILE A 222 SHEET 11 B11 VAL A 48 ALA A 52 1 O VAL A 48 N ILE A 267 LINK NZ LYS A 54 C4A PLP A 554 1555 1555 1.31 LINK LI LI A 530 O HOH A 645 1555 1555 2.74 LINK LI LI A 530 O LYS A 154 1555 1555 2.75 LINK LI LI A 530 O HIS A 151 1555 1555 2.93 LINK LI LI A 530 O SER A 152 1555 1555 2.91 LINK LI LI A 530 OD1 ASN A 156 1555 1555 2.76 LINK LI LI A 540 O SER A 384 1555 1555 2.66 LINK LI LI A 540 O HOH A 590 1555 1555 2.72 LINK LI LI A 540 ND2 ASN A 303 1555 1555 3.13 LINK LI LI A 540 O PRO A 390 1555 1555 3.06 LINK LI LI A 540 O ARG A 389 1555 1555 2.96 CISPEP 1 CYS A 26 PRO A 27 0 2.48 SITE 1 AC1 3 MES A 510 HOH A 704 HOH A 784 SITE 1 AC2 5 HIS A 151 SER A 152 LYS A 154 ASN A 156 SITE 2 AC2 5 HOH A 645 SITE 1 AC3 6 ASN A 303 SER A 384 ARG A 389 PRO A 390 SITE 2 AC3 6 LEU A 391 HOH A 590 SITE 1 AC4 16 ALA A 52 LYS A 54 THR A 100 HIS A 191 SITE 2 AC4 16 GLY A 227 GLU A 268 GLY A 270 ARG A 271 SITE 3 AC4 16 CYS A 342 TYR A 378 MES A 510 HOH A 595 SITE 4 AC4 16 HOH A 602 HOH A 614 HOH A 629 HOH A 631 SITE 1 AC5 13 LYS A 54 THR A 157 HIS A 191 TYR A 311 SITE 2 AC5 13 GLU A 343 SER A 344 TYR A 378 SO4 A 520 SITE 3 AC5 13 PLP A 554 HOH A 609 HOH A 614 HOH A 704 SITE 4 AC5 13 HOH A 864 CRYST1 98.580 98.580 176.950 90.00 90.00 120.00 P 61 2 2 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 0.010140 0.005860 0.000000 0.00000 SCALE2 0.000000 0.011710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005650 0.00000