HEADER LYASE 06-JUN-12 4FHA TITLE STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM STREPTOCOCCUS TITLE 2 PNEUMONIAE,BOUND TO PYRUVATE AND LYSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.2.1.52; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 406556; SOURCE 4 STRAIN: SP3-BS71; SOURCE 5 GENE: CGSSP3BS71_00085; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET101/D-TOPO KEYWDS 8-FOLD ALPHA-/BETA-BARREL, LYASE, L-ASPARTATE-4-SEMIALDEHYDE HYDRO- KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.PERUGINI,C.DOGOVSKI,M.W.PARKER,M.A.GORMAN REVDAT 3 29-NOV-23 4FHA 1 REMARK REVDAT 2 13-SEP-23 4FHA 1 REMARK LINK REVDAT 1 18-SEP-13 4FHA 0 JRNL AUTH M.A.PERUGINI,C.DOGOVSKI,M.W.PARKER,M.A.GORMAN,R.C.J.DOBSON, JRNL AUTH 2 G.B.JAMESON,N.E.KETAREN,J.PRASZKIER,M.F.BAILEY,G.BRYANT, JRNL AUTH 3 J.YANG,M.D.W.GRIFFIN,F.G.PEARCE,V.MITSAKOS JRNL TITL STRUCTURE, FUNCTION, STABILITY AND KNOCKOUT PHENOTYPE OF JRNL TITL 2 DIHYDRODIPICOLINATE SYNTHASE FROM STREPTOCOCCUS PNEUMONIAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 39.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 55281 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2754 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) : 2970 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 145 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4728 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 328 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.92000 REMARK 3 B22 (A**2) : -9.92000 REMARK 3 B33 (A**2) : -1.01000 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): 0.026 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.023 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.351 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4871 ; 0.005 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6622 ; 0.997 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 614 ; 5.200 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 208 ;35.650 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 782 ;12.797 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;13.905 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 759 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3706 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.438 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H, L, K REMARK 3 TWIN FRACTION : 0.562 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: AMPLITUDE BASED TWIN REFINEMENT USED REMARK 4 REMARK 4 4FHA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000072899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95371 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55338 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 75.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 27.3000 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) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : 0.34000 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3H5D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FLUORIDE, 0.1 M BIS-TRIS REMARK 280 PROPANE, 20% (W/V) PEG 3350, 5% (W/V) 1,4-DIOXANE, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.18400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.11600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.18400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.11600 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 THR A 299 REMARK 465 LYS A 300 REMARK 465 ALA A 301 REMARK 465 MET B 1 REMARK 465 THR B 299 REMARK 465 LYS B 300 REMARK 465 ALA B 301 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 TYR A 114 -55.84 73.06 REMARK 500 VAL A 147 -61.95 68.77 REMARK 500 THR A 171 -95.93 -124.02 REMARK 500 ASP A 310 32.77 -87.17 REMARK 500 THR B 85 -166.08 -122.47 REMARK 500 TYR B 114 -54.16 76.71 REMARK 500 VAL B 147 -66.15 69.46 REMARK 500 THR B 171 -112.60 -125.08 REMARK 500 ASP B 231 75.65 -106.10 REMARK 500 GLU B 297 -135.90 -110.64 REMARK 500 ASP B 310 31.53 -97.23 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 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 159 O REMARK 620 2 HIS A 161 O 100.1 REMARK 620 3 ILE A 164 O 111.1 89.6 REMARK 620 4 HOH A 655 O 112.8 141.2 96.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 159 O REMARK 620 2 HIS B 161 O 105.1 REMARK 620 3 ILE B 164 O 110.5 93.5 REMARK 620 4 HOH B 638 O 89.4 77.4 159.8 REMARK 620 5 HOH B 666 O 122.0 126.6 92.4 79.3 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 LYS A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LYS B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I7S RELATED DB: PDB REMARK 900 DIHYDRODIPICOLINATE SYNTHASE MUTANT REMARK 900 RELATED ID: 3H5D RELATED DB: PDB REMARK 900 DIHYDRODIPICOLINATE SYNTHASE FROM DRUG-RESISTANT STREPTOCOCCUS REMARK 900 PNEUMONIAE REMARK 900 RELATED ID: 3DAQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM METHICILLIN- REMARK 900 RESISTANT STAPHYLOCOCCUS AUREUS DBREF 4FHA A 1 311 UNP A5LD17 A5LD17_STRPN 1 311 DBREF 4FHA B 1 311 UNP A5LD17 A5LD17_STRPN 1 311 SEQRES 1 A 311 MET SER TYR GLN ASP LEU LYS GLU CYS LYS ILE ILE THR SEQRES 2 A 311 ALA PHE ILE THR PRO PHE HIS GLU ASP GLY SER ILE ASN SEQRES 3 A 311 PHE ASP ALA ILE PRO ALA LEU ILE GLU HIS LEU LEU ALA SEQRES 4 A 311 HIS HIS THR ASP GLY ILE LEU LEU ALA GLY THR THR ALA SEQRES 5 A 311 GLU SER PRO THR LEU THR HIS ASP GLU GLU LEU GLU LEU SEQRES 6 A 311 PHE ALA ALA VAL GLN LYS VAL VAL ASN GLY ARG VAL PRO SEQRES 7 A 311 LEU ILE ALA GLY VAL GLY THR ASN ASP THR ARG ASP SER SEQRES 8 A 311 ILE GLU PHE VAL LYS GLU VAL ALA GLU PHE GLY GLY PHE SEQRES 9 A 311 ALA ALA GLY LEU ALA ILE VAL PRO TYR TYR ASN LYS PRO SEQRES 10 A 311 SER GLN GLU GLY MET TYR GLN HIS PHE LYS ALA ILE ALA SEQRES 11 A 311 ASP ALA SER ASP LEU PRO ILE ILE ILE TYR ASN ILE PRO SEQRES 12 A 311 GLY ARG VAL VAL VAL GLU LEU THR PRO GLU THR MET LEU SEQRES 13 A 311 ARG LEU ALA ASP HIS PRO ASN ILE ILE GLY VAL KPI GLU SEQRES 14 A 311 CYS THR SER LEU ALA ASN MET ALA TYR LEU ILE GLU HIS SEQRES 15 A 311 LYS PRO GLU GLU PHE LEU ILE TYR THR GLY GLU ASP GLY SEQRES 16 A 311 ASP ALA PHE HIS ALA MET ASN LEU GLY ALA ASP GLY VAL SEQRES 17 A 311 ILE SER VAL ALA SER HIS THR ASN GLY ASP GLU MET HIS SEQRES 18 A 311 GLU MET PHE THR ALA ILE ALA GLU SER ASP MET LYS LYS SEQRES 19 A 311 ALA ALA ALA ILE GLN ARG LYS PHE ILE PRO LYS VAL ASN SEQRES 20 A 311 ALA LEU PHE SER TYR PRO SER PRO ALA PRO VAL LYS ALA SEQRES 21 A 311 ILE LEU ASN TYR MET GLY PHE GLU ALA GLY PRO THR ARG SEQRES 22 A 311 LEU PRO LEU VAL PRO ALA PRO GLU GLU ASP VAL LYS ARG SEQRES 23 A 311 ILE ILE LYS VAL VAL VAL ASP GLY ASP TYR GLU ALA THR SEQRES 24 A 311 LYS ALA THR VAL THR GLY VAL LEU ARG PRO ASP TYR SEQRES 1 B 311 MET SER TYR GLN ASP LEU LYS GLU CYS LYS ILE ILE THR SEQRES 2 B 311 ALA PHE ILE THR PRO PHE HIS GLU ASP GLY SER ILE ASN SEQRES 3 B 311 PHE ASP ALA ILE PRO ALA LEU ILE GLU HIS LEU LEU ALA SEQRES 4 B 311 HIS HIS THR ASP GLY ILE LEU LEU ALA GLY THR THR ALA SEQRES 5 B 311 GLU SER PRO THR LEU THR HIS ASP GLU GLU LEU GLU LEU SEQRES 6 B 311 PHE ALA ALA VAL GLN LYS VAL VAL ASN GLY ARG VAL PRO SEQRES 7 B 311 LEU ILE ALA GLY VAL GLY THR ASN ASP THR ARG ASP SER SEQRES 8 B 311 ILE GLU PHE VAL LYS GLU VAL ALA GLU PHE GLY GLY PHE SEQRES 9 B 311 ALA ALA GLY LEU ALA ILE VAL PRO TYR TYR ASN LYS PRO SEQRES 10 B 311 SER GLN GLU GLY MET TYR GLN HIS PHE LYS ALA ILE ALA SEQRES 11 B 311 ASP ALA SER ASP LEU PRO ILE ILE ILE TYR ASN ILE PRO SEQRES 12 B 311 GLY ARG VAL VAL VAL GLU LEU THR PRO GLU THR MET LEU SEQRES 13 B 311 ARG LEU ALA ASP HIS PRO ASN ILE ILE GLY VAL KPI GLU SEQRES 14 B 311 CYS THR SER LEU ALA ASN MET ALA TYR LEU ILE GLU HIS SEQRES 15 B 311 LYS PRO GLU GLU PHE LEU ILE TYR THR GLY GLU ASP GLY SEQRES 16 B 311 ASP ALA PHE HIS ALA MET ASN LEU GLY ALA ASP GLY VAL SEQRES 17 B 311 ILE SER VAL ALA SER HIS THR ASN GLY ASP GLU MET HIS SEQRES 18 B 311 GLU MET PHE THR ALA ILE ALA GLU SER ASP MET LYS LYS SEQRES 19 B 311 ALA ALA ALA ILE GLN ARG LYS PHE ILE PRO LYS VAL ASN SEQRES 20 B 311 ALA LEU PHE SER TYR PRO SER PRO ALA PRO VAL LYS ALA SEQRES 21 B 311 ILE LEU ASN TYR MET GLY PHE GLU ALA GLY PRO THR ARG SEQRES 22 B 311 LEU PRO LEU VAL PRO ALA PRO GLU GLU ASP VAL LYS ARG SEQRES 23 B 311 ILE ILE LYS VAL VAL VAL ASP GLY ASP TYR GLU ALA THR SEQRES 24 B 311 LYS ALA THR VAL THR GLY VAL LEU ARG PRO ASP TYR MODRES 4FHA KPI A 168 LYS MODRES 4FHA KPI B 168 LYS HET KPI A 168 14 HET KPI B 168 14 HET LYS A 401 10 HET NA A 402 1 HET LYS B 401 10 HET NA B 402 1 HETNAM KPI (2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE) HETNAM 2 KPI AMINO]HEXANOIC ACID HETNAM LYS LYSINE HETNAM NA SODIUM ION FORMUL 1 KPI 2(C9 H16 N2 O4) FORMUL 3 LYS 2(C6 H15 N2 O2 1+) FORMUL 4 NA 2(NA 1+) FORMUL 7 HOH *328(H2 O) HELIX 1 1 SER A 2 LYS A 7 1 6 HELIX 2 2 ALA A 29 ALA A 39 1 11 HELIX 3 3 GLY A 49 LEU A 57 5 9 HELIX 4 4 THR A 58 ASN A 74 1 17 HELIX 5 5 ASP A 87 GLY A 102 1 16 HELIX 6 6 SER A 118 SER A 133 1 16 HELIX 7 7 ILE A 142 VAL A 147 1 6 HELIX 8 8 THR A 151 ASP A 160 1 10 HELIX 9 9 SER A 172 LYS A 183 1 12 HELIX 10 10 GLU A 193 GLY A 195 5 3 HELIX 11 11 ASP A 196 GLY A 204 1 9 HELIX 12 12 ALA A 212 GLU A 229 1 18 HELIX 13 13 ASP A 231 PHE A 250 1 20 HELIX 14 14 PRO A 255 MET A 265 1 11 HELIX 15 15 PRO A 280 ASP A 293 1 14 HELIX 16 16 TYR B 3 LYS B 7 1 5 HELIX 17 17 ASN B 26 ASP B 28 5 3 HELIX 18 18 ALA B 29 ALA B 39 1 11 HELIX 19 19 GLU B 53 LEU B 57 5 5 HELIX 20 20 THR B 58 ASN B 74 1 17 HELIX 21 21 ASP B 87 GLY B 102 1 16 HELIX 22 22 SER B 118 SER B 133 1 16 HELIX 23 23 ILE B 142 VAL B 147 1 6 HELIX 24 24 THR B 151 ASP B 160 1 10 HELIX 25 25 SER B 172 LYS B 183 1 12 HELIX 26 26 ASP B 196 GLY B 204 1 9 HELIX 27 27 ALA B 212 GLU B 229 1 18 HELIX 28 28 ASP B 231 PHE B 250 1 20 HELIX 29 29 PRO B 255 MET B 265 1 11 HELIX 30 30 PRO B 280 ASP B 293 1 14 SHEET 1 A 9 ILE A 11 ALA A 14 0 SHEET 2 A 9 GLY A 44 LEU A 47 1 O LEU A 46 N THR A 13 SHEET 3 A 9 LEU A 79 GLY A 82 1 O ILE A 80 N LEU A 47 SHEET 4 A 9 ALA A 106 ILE A 110 1 O LEU A 108 N ALA A 81 SHEET 5 A 9 ILE A 137 ASN A 141 1 O ILE A 138 N GLY A 107 SHEET 6 A 9 ILE A 164 GLU A 169 1 O KPI A 168 N ILE A 139 SHEET 7 A 9 LEU A 188 THR A 191 1 O LEU A 188 N ILE A 165 SHEET 8 A 9 GLY A 207 SER A 210 1 O ILE A 209 N THR A 191 SHEET 9 A 9 ILE A 11 ALA A 14 1 N ILE A 12 O VAL A 208 SHEET 1 B 9 ILE B 11 ALA B 14 0 SHEET 2 B 9 GLY B 44 LEU B 47 1 O GLY B 44 N THR B 13 SHEET 3 B 9 LEU B 79 GLY B 82 1 O ILE B 80 N LEU B 47 SHEET 4 B 9 ALA B 106 ILE B 110 1 O LEU B 108 N ALA B 81 SHEET 5 B 9 ILE B 137 ASN B 141 1 O ILE B 138 N GLY B 107 SHEET 6 B 9 ILE B 164 GLU B 169 1 O KPI B 168 N ILE B 139 SHEET 7 B 9 LEU B 188 THR B 191 1 O TYR B 190 N GLU B 169 SHEET 8 B 9 GLY B 207 SER B 210 1 O ILE B 209 N THR B 191 SHEET 9 B 9 ILE B 11 ALA B 14 1 N ILE B 12 O SER B 210 LINK C VAL A 167 N KPI A 168 1555 1555 1.33 LINK C KPI A 168 N GLU A 169 1555 1555 1.33 LINK C VAL B 167 N KPI B 168 1555 1555 1.33 LINK C KPI B 168 N GLU B 169 1555 1555 1.33 LINK O ALA A 159 NA NA A 402 1555 1555 2.24 LINK O HIS A 161 NA NA A 402 1555 1555 2.24 LINK O ILE A 164 NA NA A 402 1555 1555 2.24 LINK NA NA A 402 O HOH A 655 1555 1555 2.31 LINK O ALA B 159 NA NA B 402 1555 1555 2.24 LINK O HIS B 161 NA NA B 402 1555 1555 2.24 LINK O ILE B 164 NA NA B 402 1555 1555 2.24 LINK NA NA B 402 O HOH B 638 1555 1555 2.46 LINK NA NA B 402 O HOH B 666 1555 1555 2.31 CISPEP 1 SER A 254 PRO A 255 0 7.44 CISPEP 2 LEU A 274 PRO A 275 0 12.28 CISPEP 3 SER B 254 PRO B 255 0 8.16 CISPEP 4 LEU B 274 PRO B 275 0 11.12 SITE 1 AC1 12 SER A 54 PRO A 55 LEU A 57 HIS A 59 SITE 2 AC1 12 GLU A 62 ASN A 86 TYR A 113 HOH A 538 SITE 3 AC1 12 HOH A 615 HOH A 630 ASN B 86 LYS B 401 SITE 1 AC2 4 ALA A 159 HIS A 161 ILE A 164 HOH A 655 SITE 1 AC3 12 ASN A 86 LYS A 401 SER B 54 PRO B 55 SITE 2 AC3 12 LEU B 57 HIS B 59 GLU B 62 TYR B 113 SITE 3 AC3 12 HOH B 533 HOH B 615 HOH B 616 HOH B 633 SITE 1 AC4 5 ALA B 159 HIS B 161 ILE B 164 HOH B 638 SITE 2 AC4 5 HOH B 666 CRYST1 60.381 106.368 106.232 90.00 90.00 90.00 P 2 21 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 0.016562 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009413 0.00000