HEADER LIGASE 25-AUG-13 4ME6 TITLE CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE A FROM XANTHOMONAS TITLE 2 ORYZAE PATHOVAR ORYZAE WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ALANINE--D-ALANINE LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-ALA-D-ALA LIGASE, D-ALANYLALANINE SYNTHETASE; COMPND 5 EC: 6.3.2.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS ORYZAE PV. ORYZAE; SOURCE 3 ORGANISM_TAXID: 291331; SOURCE 4 STRAIN: KACC10331; SOURCE 5 GENE: DDLA, DDL, XOO0352; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS ADP-DEPENDING ENZYME, D-ALANINE-D-ALANINE LIGASE, NUCLEOTIDE BINDING, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR T.T.N.DOAN,J.K.KIM,Y.J.AHN,B.M.LEE,L.W.KANG REVDAT 2 08-NOV-23 4ME6 1 REMARK SEQADV LINK REVDAT 1 19-FEB-14 4ME6 0 JRNL AUTH T.N.N.DOAN,J.K.KIM,H.P.T.NGO,H.T.TRAN,S.S.CHA,K.M.CHUNG, JRNL AUTH 2 K.H.HUYNH,Y.J.AHN,L.W.KANG JRNL TITL CRYSTAL STRUCTURES OF D-ALANINE-D-ALANINE LIGASE FROM JRNL TITL 2 XANTHOMONAS ORYZAE PV. ORYZAE ALONE AND IN COMPLEX WITH JRNL TITL 3 NUCLEOTIDES JRNL REF ARCH.BIOCHEM.BIOPHYS. V.545C 92 2014 JRNL REFN ISSN 0003-9861 JRNL PMID 24440607 JRNL DOI 10.1016/J.ABB.2014.01.009 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 18463 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1981 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1282 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2550 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 171 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 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): 0.255 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.211 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.147 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.619 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2618 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2586 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3558 ; 1.669 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5896 ; 0.836 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 332 ; 6.103 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;33.387 ;23.707 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 422 ;15.788 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.569 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 418 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2980 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 598 ; 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): 1343 ; 2.100 ; 2.345 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1342 ; 2.085 ; 2.343 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1670 ; 3.245 ; 3.494 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1712 ; 4.403 ; 5.386 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1275 ; 2.944 ; 2.857 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1238 ; 3.961 ; 4.116 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1849 ; 6.084 ; 6.016 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2871 ; 8.085 ;29.182 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2858 ; 8.081 ;29.163 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 REMARK 4 REMARK 4 4ME6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20817 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.61000 REMARK 200 FOR SHELL : 8.900 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: 3E5N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% (W/V) PEG 4000, 0.1M TRIS (PH REMARK 280 8.5), 0.2M MGCL2, 0.3M DIMETHYLETHYL-(3-SULFOPROPYL)-AMMONIUM, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 49.13850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.61800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.61800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.70775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.61800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.61800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.56925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.61800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.61800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.70775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.61800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.61800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.56925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.13850 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: 5850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 49.13850 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 -18 REMARK 465 GLY A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 PRO A 92 REMARK 465 GLU A 93 REMARK 465 GLN A 94 REMARK 465 ALA A 95 REMARK 465 LEU A 96 REMARK 465 ALA A 167 REMARK 465 GLY A 190 REMARK 465 SER A 191 REMARK 465 SER A 192 REMARK 465 VAL A 249 REMARK 465 HIS A 250 REMARK 465 ASP A 251 REMARK 465 ALA A 252 REMARK 465 PHE A 253 REMARK 465 TYR A 254 REMARK 465 SER A 255 REMARK 465 TYR A 256 REMARK 465 ALA A 257 REMARK 465 THR A 258 REMARK 465 LYS A 259 REMARK 465 TYR A 260 REMARK 465 ILE A 261 REMARK 465 SER A 262 REMARK 465 GLU A 263 REMARK 465 HIS A 264 REMARK 465 GLY A 265 REMARK 465 ALA A 266 REMARK 465 LEU A 366 REMARK 465 HIS A 367 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 VAL A 248 CG1 CG2 REMARK 470 GLU A 267 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 O2A ADP A 402 O HOH A 666 2.09 REMARK 500 OE2 GLU A 228 O2' ADP A 402 2.11 REMARK 500 OD2 ASP A 140 O HOH A 569 2.19 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 SER A 56 35.81 -148.98 REMARK 500 ASN A 236 -100.08 -98.35 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 302 OD2 REMARK 620 2 ADP A 402 O2A 158.4 REMARK 620 3 HOH A 552 O 55.8 102.7 REMARK 620 4 HOH A 666 O 111.9 47.0 56.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3E5N RELATED DB: PDB REMARK 900 THE APO ENZYME- D-ALANINE-D-ALANINE LIGASE REMARK 900 RELATED ID: 3R5F RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ATP REMARK 900 RELATED ID: 4L1K RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AMPPNP REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 1-21 ARE PART OF THE MATURE PROTEIN ACCORDING TO DATABASE REMARK 999 GI:122879012 (PROTEIN REF YP_198991.6). DBREF 4ME6 A 22 367 UNP Q5H614 Q5H614_XANOR 2 347 SEQADV 4ME6 MET A -18 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 GLY A -17 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 HIS A -16 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 HIS A -15 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 HIS A -14 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 HIS A -13 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 HIS A -12 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 HIS A -11 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 HIS A -10 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 SER A -9 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 SER A -8 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 GLU A -7 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 ASN A -6 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 LEU A -5 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 TYR A -4 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 PHE A -3 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 GLN A -2 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 GLY A -1 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 HIS A 0 UNP Q5H614 EXPRESSION TAG SEQADV 4ME6 MET A 1 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 ARG A 2 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 LYS A 3 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 ILE A 4 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 ARG A 5 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 VAL A 6 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 GLY A 7 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 LEU A 8 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 ILE A 9 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 PHE A 10 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 GLY A 11 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 GLY A 12 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 LYS A 13 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 SER A 14 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 ALA A 15 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 GLU A 16 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 HIS A 17 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 GLU A 18 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 VAL A 19 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 SER A 20 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 LEU A 21 UNP Q5H614 SEE REMARK 999 SEQADV 4ME6 VAL A 327 UNP Q5H614 MET 307 ENGINEERED MUTATION SEQRES 1 A 386 MET GLY HIS HIS HIS HIS HIS HIS HIS SER SER GLU ASN SEQRES 2 A 386 LEU TYR PHE GLN GLY HIS MET ARG LYS ILE ARG VAL GLY SEQRES 3 A 386 LEU ILE PHE GLY GLY LYS SER ALA GLU HIS GLU VAL SER SEQRES 4 A 386 LEU GLN SER ALA ARG ASN ILE LEU ASP ALA LEU ASP PRO SEQRES 5 A 386 GLN ARG PHE GLU PRO VAL LEU ILE GLY ILE ASP LYS GLN SEQRES 6 A 386 GLY GLN TRP HIS VAL ASN ASP PRO ASP SER PHE LEU LEU SEQRES 7 A 386 HIS ALA ASP ASP PRO ALA ARG ILE ALA LEU HIS ARG SER SEQRES 8 A 386 GLY ARG GLY VAL ALA LEU LEU PRO GLY ALA GLN GLN GLN SEQRES 9 A 386 GLN LEU ARG PRO ILE GLN PRO GLU GLN ALA LEU ALA GLN SEQRES 10 A 386 ILE ASP VAL VAL PHE PRO ILE VAL HIS GLY THR LEU GLY SEQRES 11 A 386 GLU ASP GLY SER LEU GLN GLY LEU LEU ARG MET ALA ASN SEQRES 12 A 386 LEU PRO PHE VAL GLY SER GLY VAL LEU GLY SER ALA VAL SEQRES 13 A 386 ALA MET ASP LYS ASP MET ALA LYS ARG VAL LEU ARG ASP SEQRES 14 A 386 ALA ARG LEU ALA VAL ALA PRO PHE VAL CYS PHE ASP ARG SEQRES 15 A 386 HIS THR ALA ALA HIS ALA ASP VAL ASP THR LEU ILE ALA SEQRES 16 A 386 GLN LEU GLY LEU PRO LEU PHE VAL LYS PRO ALA ASN GLN SEQRES 17 A 386 GLY SER SER VAL GLY VAL SER GLN VAL ARG THR ALA ASP SEQRES 18 A 386 ALA PHE ALA ALA ALA LEU ALA LEU ALA LEU ALA TYR ASP SEQRES 19 A 386 HIS LYS VAL LEU VAL GLU ALA ALA VAL ALA GLY ARG GLU SEQRES 20 A 386 ILE GLU CYS ALA VAL LEU GLY ASN ALA VAL PRO HIS ALA SEQRES 21 A 386 SER VAL CYS GLY GLU VAL VAL VAL HIS ASP ALA PHE TYR SEQRES 22 A 386 SER TYR ALA THR LYS TYR ILE SER GLU HIS GLY ALA GLU SEQRES 23 A 386 ILE VAL ILE PRO ALA ASP ILE ASP ALA GLN THR GLN GLN SEQRES 24 A 386 ARG ILE GLN GLN ILE ALA VAL GLN ALA TYR GLN ALA LEU SEQRES 25 A 386 GLY CYS ALA GLY MET ALA ARG VAL ASP VAL PHE LEU CYS SEQRES 26 A 386 ALA ASP GLY ARG ILE VAL ILE ASN GLU VAL ASN THR LEU SEQRES 27 A 386 PRO GLY PHE THR ARG ILE SER VAL TYR PRO LYS LEU TRP SEQRES 28 A 386 GLN ALA SER GLY LEU ASP TYR ARG GLY LEU ILE THR ARG SEQRES 29 A 386 LEU ILE GLU LEU ALA LEU GLU ARG HIS THR ASP ASP GLN SEQRES 30 A 386 LEU LEU ARG SER ALA VAL GLU LEU HIS HET MG A 401 1 HET ADP A 402 27 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 HOH *171(H2 O) HELIX 1 1 GLU A 16 LEU A 31 1 16 HELIX 2 2 GLY A 108 ASP A 113 1 6 HELIX 3 3 GLY A 114 ALA A 123 1 10 HELIX 4 4 GLY A 131 ASP A 140 1 10 HELIX 5 5 ASP A 140 ALA A 151 1 12 HELIX 6 6 ASP A 170 GLY A 179 1 10 HELIX 7 7 THR A 200 ASP A 202 5 3 HELIX 8 8 ALA A 203 ALA A 213 1 11 HELIX 9 9 ASP A 275 GLY A 294 1 20 HELIX 10 10 SER A 326 ALA A 334 1 9 HELIX 11 11 ASP A 338 SER A 362 1 25 SHEET 1 A 4 TRP A 49 ASN A 52 0 SHEET 2 A 4 PHE A 36 ILE A 43 -1 N GLY A 42 O HIS A 50 SHEET 3 A 4 ILE A 4 GLY A 11 1 N PHE A 10 O ILE A 43 SHEET 4 A 4 VAL A 101 VAL A 106 1 O ILE A 105 N ILE A 9 SHEET 1 B 2 LEU A 58 LEU A 59 0 SHEET 2 B 2 ALA A 68 LEU A 69 -1 O ALA A 68 N LEU A 59 SHEET 1 C 2 VAL A 76 LEU A 78 0 SHEET 2 C 2 LEU A 87 PRO A 89 -1 O ARG A 88 N ALA A 77 SHEET 1 D 5 ALA A 154 VAL A 155 0 SHEET 2 D 5 ILE A 311 ASN A 317 1 O ILE A 313 N ALA A 154 SHEET 3 D 5 GLY A 297 LEU A 305 -1 N ASP A 302 O GLU A 315 SHEET 4 D 5 ARG A 227 GLY A 235 -1 N VAL A 233 O ALA A 299 SHEET 5 D 5 HIS A 240 VAL A 247 -1 O HIS A 240 N LEU A 234 SHEET 1 E 4 PHE A 158 ASP A 162 0 SHEET 2 E 4 LYS A 217 ALA A 222 -1 O VAL A 218 N PHE A 161 SHEET 3 E 4 LEU A 182 PRO A 186 -1 N LYS A 185 O LEU A 219 SHEET 4 E 4 SER A 196 VAL A 198 -1 O VAL A 198 N LEU A 182 LINK OD2 ASP A 302 MG MG A 401 1555 1555 2.57 LINK MG MG A 401 O2A ADP A 402 1555 1555 2.72 LINK MG MG A 401 O HOH A 552 1555 1555 2.98 LINK MG MG A 401 O HOH A 666 1555 1555 2.51 CISPEP 1 LEU A 180 PRO A 181 0 -3.17 CISPEP 2 ILE A 270 PRO A 271 0 -4.79 SITE 1 AC1 6 ASP A 302 ASN A 314 GLU A 315 ADP A 402 SITE 2 AC1 6 HOH A 552 HOH A 666 SITE 1 AC2 12 PHE A 183 LYS A 185 GLU A 221 ALA A 222 SITE 2 AC2 12 ALA A 223 VAL A 224 GLU A 228 PHE A 304 SITE 3 AC2 12 GLU A 315 MG A 401 HOH A 575 HOH A 666 CRYST1 83.236 83.236 98.277 90.00 90.00 90.00 P 43 21 2 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 0.012014 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012014 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010175 0.00000