HEADER LYASE 08-JUL-09 3I7S TITLE DIHYDRODIPICOLINATE SYNTHASE MUTANT - K161A - WITH THE SUBSTRATE TITLE 2 PYRUVATE BOUND IN THE ACTIVE SITE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DIHYDRODIPICOLINATE SYNTHASE; COMPND 5 SYNONYM: DHDPS; COMPND 6 EC: 4.2.1.52; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: B2478, DAPA, JW2463; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: E. COLI BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJG001 KEYWDS DIHYDRODIPICOLINATE SYNTHYASE, LYSINE BIOSYNTHESIS, AMINO-ACID KEYWDS 2 BIOSYNTHESIS, DIAMINOPIMELATE BIOSYNTHESIS, LYASE, SCHIFF BASE EXPDTA X-RAY DIFFRACTION AUTHOR R.C.J.DOBSON,G.B.JAMESON,J.A.GERRARD,T.P.SOARES DA COSTA REVDAT 6 15-NOV-23 3I7S 1 ATOM REVDAT 5 06-SEP-23 3I7S 1 REMARK REVDAT 4 13-OCT-21 3I7S 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3I7S 1 VERSN REVDAT 2 07-JUL-10 3I7S 1 JRNL REVDAT 1 14-APR-10 3I7S 0 JRNL AUTH T.P.SOARES DA COSTA,A.C.MUSCROFT-TAYLOR,R.C.DOBSON, JRNL AUTH 2 S.R.DEVENISH,G.B.JAMESON,J.A.GERRARD JRNL TITL HOW ESSENTIAL IS THE 'ESSENTIAL' ACTIVE-SITE LYSINE IN JRNL TITL 2 DIHYDRODIPICOLINATE SYNTHASE? JRNL REF BIOCHIMIE V. 92 837 2010 JRNL REFN ISSN 0300-9084 JRNL PMID 20353808 JRNL DOI 10.1016/J.BIOCHI.2010.03.004 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 37802 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) : 0.196 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2019 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2794 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4360 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.19000 REMARK 3 B12 (A**2) : -0.06000 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): 0.228 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.332 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4504 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6113 ; 1.364 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 6.131 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;37.693 ;24.566 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 740 ;15.394 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;17.417 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 731 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3311 ; 0.006 ; 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): 2906 ; 0.561 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4688 ; 1.086 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1598 ; 2.013 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1425 ; 3.312 ; 4.500 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 292 REMARK 3 ORIGIN FOR THE GROUP (A): 0.1620 32.3130 -11.9510 REMARK 3 T TENSOR REMARK 3 T11: 0.0435 T22: 0.0215 REMARK 3 T33: 0.0276 T12: -0.0230 REMARK 3 T13: -0.0307 T23: 0.0189 REMARK 3 L TENSOR REMARK 3 L11: 0.3457 L22: 0.5233 REMARK 3 L33: 0.6722 L12: -0.0375 REMARK 3 L13: 0.1343 L23: 0.0137 REMARK 3 S TENSOR REMARK 3 S11: 0.0868 S12: -0.0133 S13: -0.0668 REMARK 3 S21: -0.0199 S22: 0.0116 S23: 0.0070 REMARK 3 S31: 0.0550 S32: -0.0633 S33: -0.0984 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 292 REMARK 3 ORIGIN FOR THE GROUP (A): 12.8400 61.5350 -2.3280 REMARK 3 T TENSOR REMARK 3 T11: 0.0329 T22: 0.0306 REMARK 3 T33: 0.0073 T12: -0.0030 REMARK 3 T13: -0.0031 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.4387 L22: 0.3111 REMARK 3 L33: 0.4704 L12: 0.0097 REMARK 3 L13: -0.0107 L23: 0.2416 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: 0.0000 S13: 0.0288 REMARK 3 S21: 0.0023 S22: 0.0121 S23: 0.0115 REMARK 3 S31: -0.0100 S32: -0.0265 S33: -0.0250 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3I7S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39830 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 32.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 3.420 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.27 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : 0.35000 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1YXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M POTASSIUM PHOSPHATE, PH 10, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 276K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.83333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.66667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.66667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.83333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL UNIT IS A TETRAMER, GENERATED FROM THE DIMER REMARK 300 IN THE ASSYMETRIC UNIT. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 REMARK 350 BIOMOLECULE: 2 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: 14610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 312 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 306 LIES ON A SPECIAL POSITION. 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 155 CG CD CE NZ REMARK 470 ARG A 161 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 212 CD NE CZ NH1 NH2 REMARK 470 LYS A 219 CD CE NZ REMARK 470 ARG B 161 CG CD NE CZ NH1 NH2 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 107 -44.76 74.88 REMARK 500 ALA A 210 46.72 -145.30 REMARK 500 THR B 77 16.14 -140.90 REMARK 500 TYR B 107 -52.53 77.27 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 K A 296 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 48 O REMARK 620 2 ALA A 49 O 74.4 REMARK 620 3 LEU A 51 O 74.5 101.5 REMARK 620 4 GOL A 297 O3 114.2 81.4 171.3 REMARK 620 5 GOL A 297 O3 122.1 66.4 152.0 23.0 REMARK 620 6 HOH A 360 O 74.5 110.7 126.4 58.8 81.4 REMARK 620 7 HOH A 361 O 135.2 66.3 92.5 81.1 59.6 139.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 295 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 152 O REMARK 620 2 VAL A 154 O 84.7 REMARK 620 3 LYS A 155 O 146.6 63.9 REMARK 620 4 ILE A 157 O 99.2 82.8 88.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 296 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 301 O REMARK 620 2 SER B 48 O 108.4 REMARK 620 3 ALA B 49 O 51.3 66.5 REMARK 620 4 LEU B 51 O 134.0 71.3 92.1 REMARK 620 5 HOH B 398 O 91.3 156.5 137.0 104.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 299 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 152 O REMARK 620 2 VAL B 154 O 81.6 REMARK 620 3 LYS B 155 O 146.4 67.6 REMARK 620 4 ILE B 157 O 98.5 82.6 90.8 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 GOL A 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR A 298 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 299 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 294 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 298 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 299 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I7Q RELATED DB: PDB REMARK 900 RELATED ID: 3I7R RELATED DB: PDB DBREF 3I7S A 1 292 UNP P0A6L2 DAPA_ECOLI 1 292 DBREF 3I7S B 1 292 UNP P0A6L2 DAPA_ECOLI 1 292 SEQADV 3I7S ARG A 161 UNP P0A6L2 LYS 161 ENGINEERED MUTATION SEQADV 3I7S ARG B 161 UNP P0A6L2 LYS 161 ENGINEERED MUTATION SEQRES 1 A 292 MET PHE THR GLY SER ILE VAL ALA ILE VAL THR PRO MET SEQRES 2 A 292 ASP GLU LYS GLY ASN VAL CYS ARG ALA SER LEU LYS LYS SEQRES 3 A 292 LEU ILE ASP TYR HIS VAL ALA SER GLY THR SER ALA ILE SEQRES 4 A 292 VAL SER VAL GLY THR THR GLY GLU SER ALA THR LEU ASN SEQRES 5 A 292 HIS ASP GLU HIS ALA ASP VAL VAL MET MET THR LEU ASP SEQRES 6 A 292 LEU ALA ASP GLY ARG ILE PRO VAL ILE ALA GLY THR GLY SEQRES 7 A 292 ALA ASN ALA THR ALA GLU ALA ILE SER LEU THR GLN ARG SEQRES 8 A 292 PHE ASN ASP SER GLY ILE VAL GLY CYS LEU THR VAL THR SEQRES 9 A 292 PRO TYR TYR ASN ARG PRO SER GLN GLU GLY LEU TYR GLN SEQRES 10 A 292 HIS PHE LYS ALA ILE ALA GLU HIS THR ASP LEU PRO GLN SEQRES 11 A 292 ILE LEU TYR ASN VAL PRO SER ARG THR GLY CYS ASP LEU SEQRES 12 A 292 LEU PRO GLU THR VAL GLY ARG LEU ALA LYS VAL LYS ASN SEQRES 13 A 292 ILE ILE GLY ILE ARG GLU ALA THR GLY ASN LEU THR ARG SEQRES 14 A 292 VAL ASN GLN ILE LYS GLU LEU VAL SER ASP ASP PHE VAL SEQRES 15 A 292 LEU LEU SER GLY ASP ASP ALA SER ALA LEU ASP PHE MET SEQRES 16 A 292 GLN LEU GLY GLY HIS GLY VAL ILE SER VAL THR ALA ASN SEQRES 17 A 292 VAL ALA ALA ARG ASP MET ALA GLN MET CYS LYS LEU ALA SEQRES 18 A 292 ALA GLU GLY HIS PHE ALA GLU ALA ARG VAL ILE ASN GLN SEQRES 19 A 292 ARG LEU MET PRO LEU HIS ASN LYS LEU PHE VAL GLU PRO SEQRES 20 A 292 ASN PRO ILE PRO VAL LYS TRP ALA CYS LYS GLU LEU GLY SEQRES 21 A 292 LEU VAL ALA THR ASP THR LEU ARG LEU PRO MET THR PRO SEQRES 22 A 292 ILE THR ASP SER GLY ARG GLU THR VAL ARG ALA ALA LEU SEQRES 23 A 292 LYS HIS ALA GLY LEU LEU SEQRES 1 B 292 MET PHE THR GLY SER ILE VAL ALA ILE VAL THR PRO MET SEQRES 2 B 292 ASP GLU LYS GLY ASN VAL CYS ARG ALA SER LEU LYS LYS SEQRES 3 B 292 LEU ILE ASP TYR HIS VAL ALA SER GLY THR SER ALA ILE SEQRES 4 B 292 VAL SER VAL GLY THR THR GLY GLU SER ALA THR LEU ASN SEQRES 5 B 292 HIS ASP GLU HIS ALA ASP VAL VAL MET MET THR LEU ASP SEQRES 6 B 292 LEU ALA ASP GLY ARG ILE PRO VAL ILE ALA GLY THR GLY SEQRES 7 B 292 ALA ASN ALA THR ALA GLU ALA ILE SER LEU THR GLN ARG SEQRES 8 B 292 PHE ASN ASP SER GLY ILE VAL GLY CYS LEU THR VAL THR SEQRES 9 B 292 PRO TYR TYR ASN ARG PRO SER GLN GLU GLY LEU TYR GLN SEQRES 10 B 292 HIS PHE LYS ALA ILE ALA GLU HIS THR ASP LEU PRO GLN SEQRES 11 B 292 ILE LEU TYR ASN VAL PRO SER ARG THR GLY CYS ASP LEU SEQRES 12 B 292 LEU PRO GLU THR VAL GLY ARG LEU ALA LYS VAL LYS ASN SEQRES 13 B 292 ILE ILE GLY ILE ARG GLU ALA THR GLY ASN LEU THR ARG SEQRES 14 B 292 VAL ASN GLN ILE LYS GLU LEU VAL SER ASP ASP PHE VAL SEQRES 15 B 292 LEU LEU SER GLY ASP ASP ALA SER ALA LEU ASP PHE MET SEQRES 16 B 292 GLN LEU GLY GLY HIS GLY VAL ILE SER VAL THR ALA ASN SEQRES 17 B 292 VAL ALA ALA ARG ASP MET ALA GLN MET CYS LYS LEU ALA SEQRES 18 B 292 ALA GLU GLY HIS PHE ALA GLU ALA ARG VAL ILE ASN GLN SEQRES 19 B 292 ARG LEU MET PRO LEU HIS ASN LYS LEU PHE VAL GLU PRO SEQRES 20 B 292 ASN PRO ILE PRO VAL LYS TRP ALA CYS LYS GLU LEU GLY SEQRES 21 B 292 LEU VAL ALA THR ASP THR LEU ARG LEU PRO MET THR PRO SEQRES 22 B 292 ILE THR ASP SER GLY ARG GLU THR VAL ARG ALA ALA LEU SEQRES 23 B 292 LYS HIS ALA GLY LEU LEU HET GOL A 293 6 HET GOL A 294 6 HET K A 295 1 HET K A 296 1 HET GOL A 297 12 HET PYR A 298 6 HET PO4 A 299 5 HET PO4 A 300 5 HET GOL B 293 6 HET GOL B 294 6 HET K B 295 1 HET K B 296 1 HET GOL B 297 6 HET K B 298 1 HET K B 299 1 HET GOL B 300 6 HET GOL B 301 6 HET PYR B 302 6 HET PO4 B 303 5 HETNAM GOL GLYCEROL HETNAM K POTASSIUM ION HETNAM PYR PYRUVIC ACID HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 8(C3 H8 O3) FORMUL 5 K 6(K 1+) FORMUL 8 PYR 2(C3 H4 O3) FORMUL 9 PO4 3(O4 P 3-) FORMUL 22 HOH *170(H2 O) HELIX 1 1 CYS A 20 GLY A 35 1 16 HELIX 2 2 GLU A 47 LEU A 51 5 5 HELIX 3 3 ASN A 52 ASP A 68 1 17 HELIX 4 4 ALA A 81 ARG A 91 1 11 HELIX 5 5 SER A 111 HIS A 125 1 15 HELIX 6 6 VAL A 135 GLY A 140 1 6 HELIX 7 7 LEU A 144 ALA A 152 1 9 HELIX 8 8 THR A 168 GLU A 175 1 8 HELIX 9 9 ASP A 187 ALA A 189 5 3 HELIX 10 10 SER A 190 LEU A 197 1 8 HELIX 11 11 VAL A 205 VAL A 209 5 5 HELIX 12 12 ALA A 210 GLU A 223 1 14 HELIX 13 13 HIS A 225 LEU A 243 1 19 HELIX 14 14 PRO A 249 LEU A 259 1 11 HELIX 15 15 THR A 275 ALA A 289 1 15 HELIX 16 16 CYS B 20 GLY B 35 1 16 HELIX 17 17 GLY B 43 LEU B 51 5 9 HELIX 18 18 ASN B 52 ASP B 68 1 17 HELIX 19 19 ALA B 81 ARG B 91 1 11 HELIX 20 20 SER B 111 HIS B 125 1 15 HELIX 21 21 VAL B 135 GLY B 140 1 6 HELIX 22 22 LEU B 144 LYS B 153 1 10 HELIX 23 23 THR B 168 VAL B 177 1 10 HELIX 24 24 ASP B 187 ALA B 189 5 3 HELIX 25 25 SER B 190 LEU B 197 1 8 HELIX 26 26 VAL B 205 VAL B 209 5 5 HELIX 27 27 ALA B 210 GLY B 224 1 15 HELIX 28 28 HIS B 225 LEU B 243 1 19 HELIX 29 29 PRO B 249 LEU B 259 1 11 HELIX 30 30 THR B 275 ALA B 289 1 15 SHEET 1 A 9 GLY A 4 ALA A 8 0 SHEET 2 A 9 ALA A 38 SER A 41 1 O VAL A 40 N VAL A 7 SHEET 3 A 9 VAL A 73 GLY A 76 1 O ILE A 74 N ILE A 39 SHEET 4 A 9 GLY A 99 VAL A 103 1 O LEU A 101 N ALA A 75 SHEET 5 A 9 GLN A 130 ASN A 134 1 O ILE A 131 N CYS A 100 SHEET 6 A 9 ILE A 157 GLU A 162 1 O ARG A 161 N LEU A 132 SHEET 7 A 9 VAL A 182 SER A 185 1 O LEU A 184 N ILE A 160 SHEET 8 A 9 GLY A 201 SER A 204 1 O ILE A 203 N SER A 185 SHEET 9 A 9 GLY A 4 ALA A 8 1 N ILE A 6 O SER A 204 SHEET 1 B 9 GLY B 4 ALA B 8 0 SHEET 2 B 9 ALA B 38 SER B 41 1 O VAL B 40 N VAL B 7 SHEET 3 B 9 VAL B 73 GLY B 76 1 O ILE B 74 N ILE B 39 SHEET 4 B 9 GLY B 99 VAL B 103 1 O LEU B 101 N ALA B 75 SHEET 5 B 9 GLN B 130 ASN B 134 1 O ILE B 131 N CYS B 100 SHEET 6 B 9 ILE B 157 GLU B 162 1 O ARG B 161 N LEU B 132 SHEET 7 B 9 VAL B 182 SER B 185 1 O LEU B 184 N GLU B 162 SHEET 8 B 9 GLY B 201 SER B 204 1 O ILE B 203 N SER B 185 SHEET 9 B 9 GLY B 4 ALA B 8 1 N ILE B 6 O SER B 204 LINK O SER A 48 K K A 296 1555 1555 2.90 LINK O ALA A 49 K K A 296 1555 1555 3.01 LINK O LEU A 51 K K A 296 1555 1555 2.69 LINK O ALA A 152 K K A 295 1555 1555 2.84 LINK O VAL A 154 K K A 295 1555 1555 2.76 LINK O LYS A 155 K K A 295 1555 1555 3.24 LINK O ILE A 157 K K A 295 1555 1555 2.71 LINK K K A 296 O3 AGOL A 297 1555 1555 2.86 LINK K K A 296 O3 BGOL A 297 1555 1555 3.00 LINK K K A 296 O HOH A 360 1555 1555 2.49 LINK K K A 296 O HOH A 361 1555 1555 2.77 LINK O HOH A 301 K K B 296 1555 1555 3.09 LINK O SER B 48 K K B 296 1555 1555 3.05 LINK O ALA B 49 K K B 296 1555 1555 3.29 LINK O LEU B 51 K K B 296 1555 1555 2.80 LINK OE1 GLU B 84 K K B 298 1555 1555 3.21 LINK O ALA B 152 K K B 299 1555 1555 2.58 LINK O VAL B 154 K K B 299 1555 1555 2.59 LINK O LYS B 155 K K B 299 1555 1555 3.37 LINK O ILE B 157 K K B 299 1555 1555 2.72 LINK K K B 296 O HOH B 398 1555 1555 2.99 CISPEP 1 ASN A 248 PRO A 249 0 9.14 CISPEP 2 LEU A 269 PRO A 270 0 12.89 CISPEP 3 ASN B 248 PRO B 249 0 9.10 CISPEP 4 LEU B 269 PRO B 270 0 12.00 SITE 1 AC1 10 SER A 48 ALA A 49 GLY A 78 VAL A 103 SITE 2 AC1 10 TYR A 106 GOL A 297 HOH A 337 HOH A 360 SITE 3 AC1 10 ASN B 80 TYR B 107 SITE 1 AC2 3 LYS A 174 GLU A 175 VAL A 177 SITE 1 AC3 4 ALA A 152 VAL A 154 LYS A 155 ILE A 157 SITE 1 AC4 6 SER A 48 ALA A 49 LEU A 51 GOL A 297 SITE 2 AC4 6 HOH A 360 HOH A 361 SITE 1 AC5 13 ALA A 49 ASN A 80 TYR A 106 GOL A 293 SITE 2 AC5 13 K A 296 HOH A 301 HOH A 321 HOH A 331 SITE 3 AC5 13 HOH A 360 HOH A 361 ASN B 80 TYR B 106 SITE 4 AC5 13 GOL B 293 SITE 1 AC6 10 ALA A 8 GLY A 43 THR A 44 THR A 45 SITE 2 AC6 10 LEU A 101 TYR A 133 HOH A 349 HOH A 350 SITE 3 AC6 10 HOH A 351 HOH A 363 SITE 1 AC7 2 ARG A 21 LYS A 25 SITE 1 AC8 1 ARG A 109 SITE 1 AC9 6 ASN A 80 TYR A 107 GOL A 297 SER B 48 SITE 2 AC9 6 ALA B 49 TYR B 106 SITE 1 BC1 7 ASP B 29 VAL B 32 ALA B 33 ARG B 70 SITE 2 BC1 7 HIS B 125 K B 295 GOL B 300 SITE 1 BC2 2 HIS B 125 GOL B 294 SITE 1 BC3 5 HOH A 301 SER B 48 ALA B 49 LEU B 51 SITE 2 BC3 5 HOH B 398 SITE 1 BC4 8 PRO B 110 SER B 111 GLN B 112 CYS B 141 SITE 2 BC4 8 ASP B 142 LEU B 144 GOL B 301 HOH B 322 SITE 1 BC5 1 GLU B 84 SITE 1 BC6 4 ALA B 152 VAL B 154 LYS B 155 ILE B 157 SITE 1 BC7 4 LYS B 26 ILE B 86 HIS B 125 GOL B 294 SITE 1 BC8 3 SER B 111 GLN B 112 GOL B 297 SITE 1 BC9 9 GLY B 43 THR B 44 THR B 45 LEU B 101 SITE 2 BC9 9 TYR B 133 HOH B 379 HOH B 383 HOH B 385 SITE 3 BC9 9 HOH B 403 SITE 1 CC1 1 ARG B 109 CRYST1 120.881 120.881 110.500 90.00 90.00 120.00 P 31 2 1 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008273 0.004776 0.000000 0.00000 SCALE2 0.000000 0.009552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009050 0.00000