HEADER LYASE 12-NOV-18 6N2F TITLE MESO-DIAMINOPIMELATE DECARBOXYLASE FROM ARABIDOPSIS THALIANA (ISOFORM TITLE 2 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE DECARBOXYLASE 2, CHLOROPLASTIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DAPDC 2; COMPND 5 EC: 4.1.1.20; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: LYSA2, DIDI 18A-1F, AT5G11880, F14F18.50; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS PLP, LYSINE, DECARBOXYLASE, MESO-DIAMINOPIMELATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.CROWTHER,R.C.J.DOBSON REVDAT 3 11-OCT-23 6N2F 1 REMARK REVDAT 2 27-NOV-19 6N2F 1 REMARK REVDAT 1 24-APR-19 6N2F 0 JRNL AUTH J.M.CROWTHER,P.J.CROSS,M.R.OLIVER,M.M.LEEMAN,A.J.BARTL, JRNL AUTH 2 A.W.WEATHERHEAD,R.A.NORTH,K.A.DONOVAN,S.A.KESSANS, JRNL AUTH 3 M.D.W.GRIFFIN,H.SUZUKI,A.O.HUDSON,M.KASSANMESCHEFF, JRNL AUTH 4 R.C.J.DOBSON JRNL TITL ACTIVE SITE GATING PROVIDES STEREOCHEMICAL CONTROL FOR JRNL TITL 2 MESO-DIAMINOPIMELATE DECARBOXYLASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0232 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 38060 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 + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2078 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.27 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2872 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE SET COUNT : 144 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6424 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 311 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : 0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.360 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.262 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.257 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.464 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.873 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6582 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6077 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8934 ; 1.556 ; 1.636 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14067 ; 1.250 ; 1.573 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 830 ; 7.887 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 331 ;33.719 ;22.659 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1074 ;16.266 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;19.934 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 858 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7418 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1356 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6N2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000238056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95369 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35978 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 39.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.19500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.97500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2P3E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8 MG/ML PROTEIN IN BUFFER CONTAINING REMARK 280 0.2 MM PLP AND 5 MM LYSINE MIXED IN A 1:1 RATIO WITH A RESERVOIR REMARK 280 SOLUTION CONSISTING OF 0.28 M SODIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 PROPANE PH 7.2, 25%(W/V) PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 53.99450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 PRO A 180 REMARK 465 TYR A 181 REMARK 465 VAL A 182 REMARK 465 ALA A 183 REMARK 465 THR A 184 REMARK 465 GLY A 185 REMARK 465 ASN A 186 REMARK 465 LYS A 187 REMARK 465 ASN A 188 REMARK 465 PRO B 176 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 47 CG CD CE NZ REMARK 470 ASP A 175 CG OD1 OD2 REMARK 470 GLN A 177 CG CD OE1 NE2 REMARK 470 ILE A 193 CG1 CG2 CD1 REMARK 470 ARG A 194 NE CZ NH1 NH2 REMARK 470 LYS A 197 CG CD CE NZ REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 LYS A 210 CG CD CE NZ REMARK 470 THR A 224 OG1 CG2 REMARK 470 VAL A 271 CG1 CG2 REMARK 470 LYS A 407 CG CD CE NZ REMARK 470 GLU A 417 CG CD OE1 OE2 REMARK 470 THR B 44 OG1 CG2 REMARK 470 LYS B 47 CG CD CE NZ REMARK 470 GLU B 130 CG CD OE1 OE2 REMARK 470 ASP B 175 CG OD1 OD2 REMARK 470 GLN B 177 CG CD OE1 NE2 REMARK 470 LYS B 187 CG CD CE NZ REMARK 470 GLU B 196 CG CD OE1 OE2 REMARK 470 LYS B 197 CG CD CE NZ REMARK 470 LYS B 206 CG CD CE NZ REMARK 470 LYS B 227 CG CD CE NZ REMARK 470 GLU B 240 CG CD OE1 OE2 REMARK 470 GLU B 251 CG CD OE1 OE2 REMARK 470 ASN B 318 CG OD1 ND2 REMARK 470 LYS B 321 CG CD CE NZ REMARK 470 GLU B 356 CG CD OE1 OE2 REMARK 470 GLU B 417 CG CD OE1 OE2 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 ASN A 83 116.22 -168.40 REMARK 500 PRO A 172 -153.87 -73.40 REMARK 500 VAL A 174 -40.92 -141.50 REMARK 500 ASP A 175 109.67 -41.84 REMARK 500 LYS A 190 56.22 -142.17 REMARK 500 PHE A 191 -81.55 -125.60 REMARK 500 PRO A 297 31.64 -98.10 REMARK 500 CYS A 367 32.07 -86.54 REMARK 500 CYS A 397 -71.29 -113.51 REMARK 500 LYS A 407 97.65 -69.71 REMARK 500 HIS B 21 139.53 -173.32 REMARK 500 SER B 26 175.33 -54.34 REMARK 500 GLU B 34 -120.63 56.43 REMARK 500 ASP B 173 66.01 63.18 REMARK 500 VAL B 178 157.10 177.60 REMARK 500 LEU B 333 86.39 -155.24 REMARK 500 CYS B 397 -83.94 -118.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 360 ASP A 361 148.60 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 643 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH B 768 DISTANCE = 6.18 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 501 and LYS B REMARK 800 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6N2A RELATED DB: PDB REMARK 900 6N2A IS A DIFFERENT ISOFORM OF THE SAME PROTEIN FROM THE SAME REMARK 900 ORGANISM DBREF 6N2F A 19 440 UNP Q94A94 DCDA2_ARATH 68 489 DBREF 6N2F B 19 440 UNP Q94A94 DCDA2_ARATH 68 489 SEQRES 1 A 422 PHE ASP HIS CYS PHE LYS LYS SER SER ASP GLY PHE LEU SEQRES 2 A 422 TYR CYS GLU GLY THR LYS VAL GLN ASP ILE MET GLU THR SEQRES 3 A 422 VAL GLU LYS ARG PRO PHE TYR LEU TYR SER LYS PRO GLN SEQRES 4 A 422 ILE THR ARG ASN LEU GLU ALA TYR LYS GLU ALA LEU GLU SEQRES 5 A 422 GLY VAL ARG SER VAL ILE GLY TYR ALA ILE LYS ALA ASN SEQRES 6 A 422 ASN ASN LEU LYS ILE LEU GLU HIS LEU ARG SER LEU GLY SEQRES 7 A 422 CYS GLY ALA VAL LEU VAL SER GLY ASN GLU LEU ARG LEU SEQRES 8 A 422 ALA LEU LEU ALA GLY PHE ASP PRO THR LYS CYS ILE PHE SEQRES 9 A 422 ASN GLY ASN GLY LYS SER LEU GLU ASP LEU VAL LEU ALA SEQRES 10 A 422 ALA GLN GLU GLY VAL PHE VAL ASN VAL ASP SER GLU PHE SEQRES 11 A 422 ASP LEU ASN ASN ILE VAL GLU ALA SER ARG ILE SER GLY SEQRES 12 A 422 LYS GLN VAL ASN VAL LEU LEU ARG ILE ASN PRO ASP VAL SEQRES 13 A 422 ASP PRO GLN VAL HIS PRO TYR VAL ALA THR GLY ASN LYS SEQRES 14 A 422 ASN SER LYS PHE GLY ILE ARG ASN GLU LYS LEU GLN TRP SEQRES 15 A 422 PHE LEU ASP GLU VAL LYS ALA HIS PRO LYS GLU LEU LYS SEQRES 16 A 422 LEU VAL GLY ALA HIS CYS HIS LEU GLY SER THR ILE THR SEQRES 17 A 422 LYS VAL ASP ILE PHE ARG ASP ALA ALA VAL LEU MET ILE SEQRES 18 A 422 GLU TYR ILE ASP GLU ILE ARG ARG GLN GLY PHE GLU VAL SEQRES 19 A 422 SER TYR LEU ASN ILE GLY GLY GLY LEU GLY ILE ASP TYR SEQRES 20 A 422 TYR HIS ALA GLY ALA VAL LEU PRO THR PRO MET ASP LEU SEQRES 21 A 422 ILE ASN THR VAL ARG GLU LEU VAL LEU SER ARG ASP LEU SEQRES 22 A 422 ASN LEU ILE ILE GLU PRO GLY ARG SER LEU ILE ALA ASN SEQRES 23 A 422 THR CYS CYS PHE VAL ASN HIS VAL THR GLY VAL LYS THR SEQRES 24 A 422 ASN GLY THR LYS ASN PHE ILE VAL ILE ASP GLY SER MET SEQRES 25 A 422 ALA GLU LEU ILE ARG PRO SER LEU TYR ASP ALA TYR GLN SEQRES 26 A 422 HIS ILE GLU LEU VAL SER PRO THR PRO PRO GLU ALA GLU SEQRES 27 A 422 VAL THR LYS PHE ASP VAL VAL GLY PRO VAL CYS GLU SER SEQRES 28 A 422 ALA ASP PHE LEU GLY LYS ASP ARG GLU LEU PRO THR PRO SEQRES 29 A 422 PRO GLN GLY ALA GLY LEU VAL VAL HIS ASP ALA GLY ALA SEQRES 30 A 422 TYR CYS MET SER MET ALA SER THR TYR ASN LEU LYS MET SEQRES 31 A 422 ARG PRO PRO GLU TYR TRP VAL GLU GLU ASP GLY SER ILE SEQRES 32 A 422 THR LYS ILE ARG HIS ALA GLU THR PHE ASP ASP HIS LEU SEQRES 33 A 422 ARG PHE PHE GLU GLY LEU SEQRES 1 B 422 PHE ASP HIS CYS PHE LYS LYS SER SER ASP GLY PHE LEU SEQRES 2 B 422 TYR CYS GLU GLY THR LYS VAL GLN ASP ILE MET GLU THR SEQRES 3 B 422 VAL GLU LYS ARG PRO PHE TYR LEU TYR SER LYS PRO GLN SEQRES 4 B 422 ILE THR ARG ASN LEU GLU ALA TYR LYS GLU ALA LEU GLU SEQRES 5 B 422 GLY VAL ARG SER VAL ILE GLY TYR ALA ILE LYS ALA ASN SEQRES 6 B 422 ASN ASN LEU LYS ILE LEU GLU HIS LEU ARG SER LEU GLY SEQRES 7 B 422 CYS GLY ALA VAL LEU VAL SER GLY ASN GLU LEU ARG LEU SEQRES 8 B 422 ALA LEU LEU ALA GLY PHE ASP PRO THR LYS CYS ILE PHE SEQRES 9 B 422 ASN GLY ASN GLY LYS SER LEU GLU ASP LEU VAL LEU ALA SEQRES 10 B 422 ALA GLN GLU GLY VAL PHE VAL ASN VAL ASP SER GLU PHE SEQRES 11 B 422 ASP LEU ASN ASN ILE VAL GLU ALA SER ARG ILE SER GLY SEQRES 12 B 422 LYS GLN VAL ASN VAL LEU LEU ARG ILE ASN PRO ASP VAL SEQRES 13 B 422 ASP PRO GLN VAL HIS PRO TYR VAL ALA THR GLY ASN LYS SEQRES 14 B 422 ASN SER LYS PHE GLY ILE ARG ASN GLU LYS LEU GLN TRP SEQRES 15 B 422 PHE LEU ASP GLU VAL LYS ALA HIS PRO LYS GLU LEU LYS SEQRES 16 B 422 LEU VAL GLY ALA HIS CYS HIS LEU GLY SER THR ILE THR SEQRES 17 B 422 LYS VAL ASP ILE PHE ARG ASP ALA ALA VAL LEU MET ILE SEQRES 18 B 422 GLU TYR ILE ASP GLU ILE ARG ARG GLN GLY PHE GLU VAL SEQRES 19 B 422 SER TYR LEU ASN ILE GLY GLY GLY LEU GLY ILE ASP TYR SEQRES 20 B 422 TYR HIS ALA GLY ALA VAL LEU PRO THR PRO MET ASP LEU SEQRES 21 B 422 ILE ASN THR VAL ARG GLU LEU VAL LEU SER ARG ASP LEU SEQRES 22 B 422 ASN LEU ILE ILE GLU PRO GLY ARG SER LEU ILE ALA ASN SEQRES 23 B 422 THR CYS CYS PHE VAL ASN HIS VAL THR GLY VAL LYS THR SEQRES 24 B 422 ASN GLY THR LYS ASN PHE ILE VAL ILE ASP GLY SER MET SEQRES 25 B 422 ALA GLU LEU ILE ARG PRO SER LEU TYR ASP ALA TYR GLN SEQRES 26 B 422 HIS ILE GLU LEU VAL SER PRO THR PRO PRO GLU ALA GLU SEQRES 27 B 422 VAL THR LYS PHE ASP VAL VAL GLY PRO VAL CYS GLU SER SEQRES 28 B 422 ALA ASP PHE LEU GLY LYS ASP ARG GLU LEU PRO THR PRO SEQRES 29 B 422 PRO GLN GLY ALA GLY LEU VAL VAL HIS ASP ALA GLY ALA SEQRES 30 B 422 TYR CYS MET SER MET ALA SER THR TYR ASN LEU LYS MET SEQRES 31 B 422 ARG PRO PRO GLU TYR TRP VAL GLU GLU ASP GLY SER ILE SEQRES 32 B 422 THR LYS ILE ARG HIS ALA GLU THR PHE ASP ASP HIS LEU SEQRES 33 B 422 ARG PHE PHE GLU GLY LEU HET PLP B 501 15 HET LYS B 502 10 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM LYS LYSINE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PLP C8 H10 N O6 P FORMUL 4 LYS C6 H15 N2 O2 1+ FORMUL 5 HOH *311(H2 O) HELIX 1 AA1 VAL A 38 VAL A 45 1 8 HELIX 2 AA2 LYS A 55 LEU A 69 1 15 HELIX 3 AA3 ASN A 85 LEU A 95 1 11 HELIX 4 AA4 SER A 103 ALA A 113 1 11 HELIX 5 AA5 ASP A 116 THR A 118 5 3 HELIX 6 AA6 SER A 128 GLY A 139 1 12 HELIX 7 AA7 SER A 146 GLY A 161 1 16 HELIX 8 AA8 LYS A 197 ALA A 207 1 11 HELIX 9 AA9 LYS A 227 GLN A 248 1 22 HELIX 10 AB1 THR A 274 THR A 281 1 8 HELIX 11 AB2 VAL A 282 ASP A 290 1 9 HELIX 12 AB3 PRO A 297 ALA A 303 1 7 HELIX 13 AB4 ILE A 334 ASP A 340 1 7 HELIX 14 AB5 CYS A 397 ALA A 401 5 5 HELIX 15 AB6 THR A 403 LYS A 407 5 5 HELIX 16 AB7 THR A 429 ARG A 435 1 7 HELIX 17 AB8 PHE A 436 GLU A 438 5 3 HELIX 18 AB9 VAL B 38 THR B 44 1 7 HELIX 19 AC1 LYS B 55 LEU B 69 1 15 HELIX 20 AC2 LYS B 81 ASN B 83 5 3 HELIX 21 AC3 ASN B 85 LEU B 95 1 11 HELIX 22 AC4 SER B 103 ALA B 113 1 11 HELIX 23 AC5 ASP B 116 THR B 118 5 3 HELIX 24 AC6 SER B 128 GLY B 139 1 12 HELIX 25 AC7 SER B 146 GLY B 161 1 16 HELIX 26 AC8 HIS B 179 ALA B 183 5 5 HELIX 27 AC9 LYS B 197 ALA B 207 1 11 HELIX 28 AD1 VAL B 228 GLN B 248 1 21 HELIX 29 AD2 THR B 274 ASN B 280 1 7 HELIX 30 AD3 VAL B 282 ARG B 289 1 8 HELIX 31 AD4 GLY B 298 ALA B 303 1 6 HELIX 32 AD5 ILE B 334 ASP B 340 1 7 HELIX 33 AD6 CYS B 397 ALA B 401 5 5 HELIX 34 AD7 THR B 403 LYS B 407 5 5 HELIX 35 AD8 PHE B 430 ARG B 435 1 6 HELIX 36 AD9 PHE B 436 GLU B 438 5 3 SHEET 1 AA1 3 PHE A 23 LYS A 25 0 SHEET 2 AA1 3 LEU A 31 CYS A 33 -1 O TYR A 32 N LYS A 24 SHEET 3 AA1 3 THR A 36 LYS A 37 -1 O THR A 36 N CYS A 33 SHEET 1 AA2 6 ILE A 345 LEU A 347 0 SHEET 2 AA2 6 GLY A 387 VAL A 390 -1 O VAL A 389 N GLU A 346 SHEET 3 AA2 6 CYS A 306 ASN A 318 -1 N ASN A 310 O LEU A 388 SHEET 4 AA2 6 LYS A 321 ILE A 326 -1 O VAL A 325 N GLY A 314 SHEET 5 AA2 6 VAL A 357 VAL A 363 1 O VAL A 363 N ILE A 326 SHEET 6 AA2 6 PHE A 372 PRO A 380 -1 O ARG A 377 N PHE A 360 SHEET 1 AA3 6 ILE A 345 LEU A 347 0 SHEET 2 AA3 6 GLY A 387 VAL A 390 -1 O VAL A 389 N GLU A 346 SHEET 3 AA3 6 CYS A 306 ASN A 318 -1 N ASN A 310 O LEU A 388 SHEET 4 AA3 6 PHE A 50 SER A 54 -1 N LEU A 52 O CYS A 307 SHEET 5 AA3 6 GLU A 412 VAL A 415 1 O TYR A 413 N TYR A 53 SHEET 6 AA3 6 ILE A 421 ARG A 425 -1 O THR A 422 N TRP A 414 SHEET 1 AA4 9 SER A 74 ALA A 79 0 SHEET 2 AA4 9 GLY A 98 LEU A 101 1 O GLY A 98 N ILE A 76 SHEET 3 AA4 9 CYS A 120 PHE A 122 1 O ILE A 121 N LEU A 101 SHEET 4 AA4 9 PHE A 141 VAL A 144 1 O ASN A 143 N PHE A 122 SHEET 5 AA4 9 VAL A 164 ARG A 169 1 O LEU A 167 N VAL A 144 SHEET 6 AA4 9 LEU A 212 ILE A 225 1 O VAL A 215 N VAL A 166 SHEET 7 AA4 9 TYR A 254 LEU A 261 1 O GLY A 260 N ILE A 225 SHEET 8 AA4 9 ASN A 292 GLU A 296 1 O ILE A 294 N LEU A 255 SHEET 9 AA4 9 SER A 74 ALA A 79 1 N GLY A 77 O ILE A 295 SHEET 1 AA5 3 PHE B 23 LYS B 25 0 SHEET 2 AA5 3 LEU B 31 CYS B 33 -1 O TYR B 32 N LYS B 24 SHEET 3 AA5 3 THR B 36 LYS B 37 -1 O THR B 36 N CYS B 33 SHEET 1 AA6 6 ILE B 345 LEU B 347 0 SHEET 2 AA6 6 GLY B 387 VAL B 390 -1 O VAL B 389 N GLU B 346 SHEET 3 AA6 6 CYS B 306 ASN B 318 -1 N ASN B 310 O LEU B 388 SHEET 4 AA6 6 LYS B 321 ILE B 326 -1 O VAL B 325 N THR B 313 SHEET 5 AA6 6 THR B 358 VAL B 363 1 O ASP B 361 N ASN B 322 SHEET 6 AA6 6 PHE B 372 LEU B 379 -1 O GLY B 374 N VAL B 362 SHEET 1 AA7 6 ILE B 345 LEU B 347 0 SHEET 2 AA7 6 GLY B 387 VAL B 390 -1 O VAL B 389 N GLU B 346 SHEET 3 AA7 6 CYS B 306 ASN B 318 -1 N ASN B 310 O LEU B 388 SHEET 4 AA7 6 PHE B 50 SER B 54 -1 N PHE B 50 O VAL B 309 SHEET 5 AA7 6 GLU B 412 VAL B 415 1 O VAL B 415 N TYR B 53 SHEET 6 AA7 6 ILE B 421 ARG B 425 -1 O THR B 422 N TRP B 414 SHEET 1 AA8 9 SER B 74 ALA B 79 0 SHEET 2 AA8 9 GLY B 98 LEU B 101 1 O GLY B 98 N ILE B 76 SHEET 3 AA8 9 CYS B 120 PHE B 122 1 O ILE B 121 N LEU B 101 SHEET 4 AA8 9 PHE B 141 VAL B 144 1 O PHE B 141 N PHE B 122 SHEET 5 AA8 9 VAL B 164 ARG B 169 1 O ASN B 165 N VAL B 142 SHEET 6 AA8 9 LEU B 212 HIS B 218 1 O HIS B 218 N LEU B 168 SHEET 7 AA8 9 TYR B 254 GLY B 258 1 O ASN B 256 N ALA B 217 SHEET 8 AA8 9 ASN B 292 ILE B 295 1 O ILE B 294 N LEU B 255 SHEET 9 AA8 9 SER B 74 ALA B 79 1 N GLY B 77 O ILE B 295 LINK C4A PLP B 501 NZ LYS B 502 1555 1555 1.28 SITE 1 AC1 21 CYS A 367 GLU A 368 TYR A 404 ALA B 79 SITE 2 AC1 21 LYS B 81 ASN B 123 VAL B 182 HIS B 220 SITE 3 AC1 21 SER B 223 GLY B 259 GLY B 260 GLU B 296 SITE 4 AC1 21 PRO B 297 GLY B 298 ARG B 299 ARG B 335 SITE 5 AC1 21 TYR B 339 TYR B 396 HOH B 605 HOH B 617 SITE 6 AC1 21 HOH B 624 CRYST1 51.381 107.989 80.929 90.00 98.61 90.00 P 1 21 1 4 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 0.019462 0.000000 0.002946 0.00000 SCALE2 0.000000 0.009260 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012497 0.00000