HEADER LYASE 12-NOV-18 6N2A TITLE MESO-DIAMINOPIMELATE DECARBOXYLASE FROM ARABIDOPSIS THALIANA (ISOFORM TITLE 2 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE DECARBOXYLASE 1, CHLOROPLASTIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DAPDC 1; 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: LYSA1, AT3G14390, MLN21.17; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET30A; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A::AT3G14390 KEYWDS PLP, LYSINE, DECARBOXYLASE, MESO-DIAMINOPIMELATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.CROWTHER,R.C.J.DOBSON REVDAT 3 11-OCT-23 6N2A 1 REMARK REVDAT 2 27-NOV-19 6N2A 1 REMARK REVDAT 1 24-APR-19 6N2A 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. 1.88 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 69528 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2260 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) : 1.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5049 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 163 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6451 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 696 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.937 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6706 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6193 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9104 ; 1.573 ; 1.638 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14370 ; 1.384 ; 1.573 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 848 ; 7.499 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 348 ;33.602 ;22.759 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1125 ;14.640 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;17.428 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 865 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7597 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1373 ; 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 6N2A 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_1000238028. 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 : 7.5 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 : 71841 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 42.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.14700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.30100 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 (%): 47.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8 MG/ML PROTEIN IN BUFFER CONTAINING REMARK 280 0.2 MM PLP AND 0.4 MM LYSINE MIXED IN A 1:1 RATIO WITH A REMARK 280 RESERVOIR SOLUTION CONSISTING OF 0.2 M MAGNESIUM CHLORIDE, 0.1 M REMARK 280 TRIS PH 7.5, 20%(W/V) PEG 6000., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.48400 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.79350 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.48400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.79350 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: 8150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 966 LIES ON A SPECIAL POSITION. 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 VAL B 170 REMARK 465 ASP B 171 REMARK 465 PRO B 172 REMARK 465 GLN B 173 REMARK 465 VAL B 174 REMARK 465 HIS B 175 REMARK 465 PRO B 176 REMARK 465 TYR B 177 REMARK 465 VAL B 178 REMARK 465 ALA B 179 REMARK 465 THR B 180 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 PHE A 15 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 183 CD CE NZ REMARK 470 LYS A 193 CD CE NZ REMARK 470 LYS A 223 CD CE NZ REMARK 470 GLU A 350 CG CD OE1 OE2 REMARK 470 GLU A 352 CG CD OE1 OE2 REMARK 470 PHE B 15 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 20 CD CE NZ REMARK 470 ARG B 43 NE CZ NH1 NH2 REMARK 470 LYS B 62 CD CE NZ REMARK 470 LYS B 158 CE NZ REMARK 470 ASP B 169 CG OD1 OD2 REMARK 470 LYS B 183 CG CD CE NZ REMARK 470 LYS B 223 CD CE NZ REMARK 470 GLU B 247 CG CD OE1 OE2 REMARK 470 GLU B 350 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 77 C4A PLP A 501 1.99 REMARK 500 OE2 GLU A 236 O HOH A 601 2.06 REMARK 500 OE2 GLU A 151 O HOH A 602 2.12 REMARK 500 O HOH A 669 O HOH A 917 2.15 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 421 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 421 NE - CZ - NH2 ANGL. DEV. = -5.3 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 ASP A 16 20.44 46.86 REMARK 500 ASN A 79 119.88 -174.67 REMARK 500 GLU A 350 -11.34 93.92 REMARK 500 CYS A 363 11.15 -65.49 REMARK 500 CYS A 393 -81.71 -112.53 REMARK 500 ASP B 16 38.77 -90.06 REMARK 500 ASN B 182 -39.55 -162.94 REMARK 500 GLU B 350 1.04 82.20 REMARK 500 CYS B 363 25.99 -77.37 REMARK 500 CYS B 393 -81.30 -116.40 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 B 919 DISTANCE = 6.02 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 A 501 and LYS A REMARK 800 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 501 and LYS B REMARK 800 502 DBREF 6N2A A 15 436 UNP Q949X7 DCDA1_ARATH 63 484 DBREF 6N2A B 15 436 UNP Q949X7 DCDA1_ARATH 63 484 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 GLU ASP ILE MET GLU SER SEQRES 3 A 422 VAL GLU ARG 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 SER 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 ARG 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 GLN 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 PRO PRO ALA 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 GLU ASP ILE MET GLU SER SEQRES 3 B 422 VAL GLU ARG 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 SER 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 ARG 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 GLN 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 PRO PRO ALA 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 A 501 15 HET LYS A 502 10 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 2(C8 H10 N O6 P) FORMUL 4 LYS 2(C6 H15 N2 O2 1+) FORMUL 7 HOH *696(H2 O) HELIX 1 AA1 VAL A 34 VAL A 41 1 8 HELIX 2 AA2 LYS A 51 LEU A 65 1 15 HELIX 3 AA3 LYS A 77 ASN A 79 5 3 HELIX 4 AA4 ASN A 81 LEU A 91 1 11 HELIX 5 AA5 SER A 99 ALA A 109 1 11 HELIX 6 AA6 ASP A 112 THR A 114 5 3 HELIX 7 AA7 SER A 124 GLY A 135 1 12 HELIX 8 AA8 SER A 142 GLY A 157 1 16 HELIX 9 AA9 HIS A 175 SER A 185 1 11 HELIX 10 AB1 LYS A 193 HIS A 204 1 12 HELIX 11 AB2 VAL A 224 GLN A 244 1 21 HELIX 12 AB3 THR A 270 THR A 277 1 8 HELIX 13 AB4 VAL A 278 ASP A 286 1 9 HELIX 14 AB5 GLY A 294 ALA A 299 1 6 HELIX 15 AB6 ILE A 330 ASP A 336 1 7 HELIX 16 AB7 CYS A 393 ALA A 397 5 5 HELIX 17 AB8 THR A 399 LYS A 403 5 5 HELIX 18 AB9 THR A 425 ARG A 431 1 7 HELIX 19 AC1 PHE A 432 GLU A 434 5 3 HELIX 20 AC2 VAL B 34 SER B 40 1 7 HELIX 21 AC3 LYS B 51 LEU B 65 1 15 HELIX 22 AC4 LYS B 77 ASN B 79 5 3 HELIX 23 AC5 ASN B 81 LEU B 91 1 11 HELIX 24 AC6 SER B 99 ALA B 109 1 11 HELIX 25 AC7 ASP B 112 THR B 114 5 3 HELIX 26 AC8 SER B 124 GLY B 135 1 12 HELIX 27 AC9 SER B 142 GLY B 157 1 16 HELIX 28 AD1 ARG B 190 GLU B 192 5 3 HELIX 29 AD2 LYS B 193 ALA B 203 1 11 HELIX 30 AD3 VAL B 224 GLN B 244 1 21 HELIX 31 AD4 THR B 270 THR B 277 1 8 HELIX 32 AD5 VAL B 278 ARG B 285 1 8 HELIX 33 AD6 GLY B 294 ALA B 299 1 6 HELIX 34 AD7 ILE B 330 ASP B 336 1 7 HELIX 35 AD8 CYS B 393 ALA B 397 5 5 HELIX 36 AD9 THR B 399 LYS B 403 5 5 HELIX 37 AE1 THR B 425 ARG B 431 1 7 HELIX 38 AE2 PHE B 432 GLU B 434 5 3 SHEET 1 AA1 3 PHE A 19 LYS A 21 0 SHEET 2 AA1 3 LEU A 27 CYS A 29 -1 O TYR A 28 N LYS A 20 SHEET 3 AA1 3 THR A 32 LYS A 33 -1 O THR A 32 N CYS A 29 SHEET 1 AA2 6 ILE A 341 LEU A 343 0 SHEET 2 AA2 6 GLY A 383 VAL A 386 -1 O VAL A 385 N GLU A 342 SHEET 3 AA2 6 CYS A 302 THR A 313 -1 N ASN A 306 O LEU A 384 SHEET 4 AA2 6 ASN A 318 ILE A 322 -1 O VAL A 321 N GLY A 310 SHEET 5 AA2 6 VAL A 353 VAL A 359 1 O VAL A 359 N ILE A 322 SHEET 6 AA2 6 PHE A 368 PRO A 376 -1 O LEU A 369 N VAL A 358 SHEET 1 AA3 6 ILE A 341 LEU A 343 0 SHEET 2 AA3 6 GLY A 383 VAL A 386 -1 O VAL A 385 N GLU A 342 SHEET 3 AA3 6 CYS A 302 THR A 313 -1 N ASN A 306 O LEU A 384 SHEET 4 AA3 6 PHE A 46 SER A 50 -1 N PHE A 46 O VAL A 305 SHEET 5 AA3 6 GLU A 408 VAL A 411 1 O VAL A 411 N TYR A 49 SHEET 6 AA3 6 ILE A 417 ARG A 421 -1 O THR A 418 N TRP A 410 SHEET 1 AA410 ILE A 189 ARG A 190 0 SHEET 2 AA410 VAL A 160 ASN A 167 1 N ASN A 167 O ILE A 189 SHEET 3 AA410 LEU A 208 HIS A 214 1 O VAL A 211 N VAL A 162 SHEET 4 AA410 TYR A 250 ASN A 252 1 O ASN A 252 N ALA A 213 SHEET 5 AA410 ASN A 288 ILE A 291 1 O ILE A 290 N LEU A 251 SHEET 6 AA410 SER A 70 ALA A 75 1 N GLY A 73 O ILE A 291 SHEET 7 AA410 GLY A 94 LEU A 97 1 O GLY A 94 N ILE A 72 SHEET 8 AA410 CYS A 116 PHE A 118 1 O ILE A 117 N LEU A 97 SHEET 9 AA410 PHE A 137 VAL A 140 1 O PHE A 137 N PHE A 118 SHEET 10 AA410 VAL A 160 ASN A 167 1 O ARG A 165 N VAL A 140 SHEET 1 AA5 3 PHE B 19 LYS B 21 0 SHEET 2 AA5 3 LEU B 27 CYS B 29 -1 O TYR B 28 N LYS B 20 SHEET 3 AA5 3 THR B 32 LYS B 33 -1 O THR B 32 N CYS B 29 SHEET 1 AA6 6 ILE B 341 LEU B 343 0 SHEET 2 AA6 6 GLY B 383 VAL B 386 -1 O VAL B 385 N GLU B 342 SHEET 3 AA6 6 CYS B 302 ASN B 314 -1 N ASN B 306 O LEU B 384 SHEET 4 AA6 6 LYS B 317 ILE B 322 -1 O VAL B 321 N GLY B 310 SHEET 5 AA6 6 VAL B 353 VAL B 359 1 O ASP B 357 N ILE B 320 SHEET 6 AA6 6 PHE B 368 PRO B 376 -1 O GLY B 370 N VAL B 358 SHEET 1 AA7 6 ILE B 341 LEU B 343 0 SHEET 2 AA7 6 GLY B 383 VAL B 386 -1 O VAL B 385 N GLU B 342 SHEET 3 AA7 6 CYS B 302 ASN B 314 -1 N ASN B 306 O LEU B 384 SHEET 4 AA7 6 PHE B 46 SER B 50 -1 N PHE B 46 O VAL B 305 SHEET 5 AA7 6 GLU B 408 VAL B 411 1 O TYR B 409 N TYR B 49 SHEET 6 AA7 6 ILE B 417 ARG B 421 -1 O ILE B 420 N GLU B 408 SHEET 1 AA8 9 SER B 70 ALA B 75 0 SHEET 2 AA8 9 GLY B 94 LEU B 97 1 O GLY B 94 N ILE B 72 SHEET 3 AA8 9 CYS B 116 PHE B 118 1 O ILE B 117 N LEU B 97 SHEET 4 AA8 9 PHE B 137 VAL B 140 1 O PHE B 137 N PHE B 118 SHEET 5 AA8 9 VAL B 160 ARG B 165 1 O ARG B 165 N VAL B 140 SHEET 6 AA8 9 LEU B 208 HIS B 214 1 O VAL B 211 N VAL B 162 SHEET 7 AA8 9 TYR B 250 ASN B 252 1 O ASN B 252 N ALA B 213 SHEET 8 AA8 9 ASN B 288 ILE B 291 1 O ASN B 288 N LEU B 251 SHEET 9 AA8 9 SER B 70 ALA B 75 1 N GLY B 73 O ILE B 291 LINK C4A PLP A 501 NZ LYS A 502 1555 1555 1.30 LINK C4A PLP B 501 NZ LYS B 502 1555 1555 1.27 SITE 1 AC1 19 LYS A 77 HIS A 216 SER A 219 GLY A 256 SITE 2 AC1 19 GLU A 292 PRO A 293 GLY A 294 ARG A 295 SITE 3 AC1 19 ARG A 331 TYR A 335 TYR A 392 HOH A 620 SITE 4 AC1 19 HOH A 632 HOH A 671 HOH A 719 HOH A 744 SITE 5 AC1 19 CYS B 363 GLU B 364 TYR B 400 SITE 1 AC2 19 CYS A 363 GLU A 364 TYR A 400 ALA B 75 SITE 2 AC2 19 LYS B 77 HIS B 216 SER B 219 GLY B 256 SITE 3 AC2 19 GLU B 292 PRO B 293 GLY B 294 ARG B 295 SITE 4 AC2 19 ARG B 331 TYR B 335 TYR B 392 HOH B 648 SITE 5 AC2 19 HOH B 664 HOH B 671 HOH B 808 CRYST1 80.968 88.624 121.587 90.00 90.00 90.00 P 21 2 21 8 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 0.012351 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011284 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008225 0.00000