HEADER LYASE 08-JUL-09 3I7R TITLE DIHYDRODIPICOLINATE SYNTHASE - K161R 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 STRAIN: E. COLI; SOURCE 5 GENE: B2478, DAPA, JW2463; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: E. COLI BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PJG001 KEYWDS DIHYDRODIPICOLINATE SYNTHASE, 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 5 06-SEP-23 3I7R 1 REMARK REVDAT 4 13-OCT-21 3I7R 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3I7R 1 VERSN REVDAT 2 07-JUL-10 3I7R 1 JRNL REVDAT 1 14-APR-10 3I7R 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 51217 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2739 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) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3836 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 196 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4381 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 396 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) : 24.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : 0.33000 REMARK 3 B12 (A**2) : -0.11000 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): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.799 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4568 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6209 ; 1.284 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 598 ; 5.735 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;35.685 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 766 ;14.449 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;17.200 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 739 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3392 ; 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): 2948 ; 0.490 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4769 ; 0.947 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1620 ; 1.753 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1440 ; 2.880 ; 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): 28.3320 -16.0180 -6.7240 REMARK 3 T TENSOR REMARK 3 T11: 0.0175 T22: 0.0655 REMARK 3 T33: 0.0236 T12: -0.0097 REMARK 3 T13: 0.0049 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 0.4962 L22: 0.6326 REMARK 3 L33: 0.7991 L12: -0.0444 REMARK 3 L13: -0.0736 L23: -0.2088 REMARK 3 S TENSOR REMARK 3 S11: 0.0024 S12: 0.0136 S13: 0.0108 REMARK 3 S21: 0.0348 S22: 0.0930 S23: 0.0898 REMARK 3 S31: 0.0188 S32: -0.0851 S33: -0.0954 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): 60.0240 -19.6530 -16.4090 REMARK 3 T TENSOR REMARK 3 T11: 0.0411 T22: 0.0462 REMARK 3 T33: 0.0067 T12: 0.0002 REMARK 3 T13: -0.0045 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.5337 L22: 0.5647 REMARK 3 L33: 0.6066 L12: 0.0809 REMARK 3 L13: -0.2076 L23: 0.1124 REMARK 3 S TENSOR REMARK 3 S11: 0.0006 S12: -0.0037 S13: -0.0495 REMARK 3 S21: 0.0063 S22: 0.0046 S23: -0.0331 REMARK 3 S31: 0.0496 S32: -0.0099 S33: -0.0052 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 3I7R 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_1000054070. 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 : 53975 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 34.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 7.070 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : 0.11400 REMARK 200 FOR THE DATA SET : 8.8000 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) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.04 REMARK 200 R MERGE FOR SHELL (I) : 0.44300 REMARK 200 R SYM FOR SHELL (I) : 0.44300 REMARK 200 FOR SHELL : 3.300 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: PDB ENTRY 1YXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 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 37.01233 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 74.02467 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 74.02467 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 37.01233 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 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: 5490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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: 13090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 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 -37.01233 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 CD CE NZ 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 -50.68 77.89 REMARK 500 PRO B 105 132.59 -39.24 REMARK 500 TYR B 107 -48.48 78.97 REMARK 500 VAL B 135 75.28 -151.07 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 294 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 48 O REMARK 620 2 ALA A 49 O 72.8 REMARK 620 3 LEU A 51 O 76.5 95.5 REMARK 620 4 GOL A 295 O3 112.4 55.7 141.3 REMARK 620 5 GOL A 295 O3 108.1 81.0 172.9 32.2 REMARK 620 6 HOH A 440 O 144.1 142.4 100.2 92.6 79.3 REMARK 620 7 HOH A 469 O 133.0 62.8 92.6 52.8 80.3 82.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 293 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 152 O REMARK 620 2 VAL A 154 O 83.5 REMARK 620 3 LYS A 155 O 144.2 63.9 REMARK 620 4 ILE A 157 O 95.4 79.6 92.8 REMARK 620 5 HOH A 428 O 110.0 162.0 105.1 87.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 294 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 123 O REMARK 620 2 GLU B 124 O 70.8 REMARK 620 3 THR B 126 O 68.6 91.2 REMARK 620 4 HOH B 343 O 128.3 83.7 67.8 REMARK 620 5 HOH B 378 O 121.8 155.7 76.6 72.3 REMARK 620 6 HOH B 438 O 66.1 101.6 125.0 165.5 102.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 293 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 152 O REMARK 620 2 VAL B 154 O 82.9 REMARK 620 3 LYS B 155 O 144.9 66.5 REMARK 620 4 ILE B 157 O 100.2 82.2 92.4 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 K A 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL 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 GOL A 298 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL 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 K B 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 294 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 297 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I7Q RELATED DB: PDB REMARK 900 K161A MUTATION DBREF 3I7R A 1 292 UNP P0A6L2 DAPA_ECOLI 1 292 DBREF 3I7R B 1 292 UNP P0A6L2 DAPA_ECOLI 1 292 SEQADV 3I7R ARG A 161 UNP P0A6L2 LYS 161 ENGINEERED MUTATION SEQADV 3I7R 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 K A 293 1 HET K A 294 1 HET GOL A 295 12 HET GOL A 296 6 HET GOL A 297 6 HET GOL A 298 6 HET CL A 299 1 HET PO4 A 300 5 HET K B 293 1 HET K B 294 1 HET GOL B 295 6 HET GOL B 296 6 HET CL B 297 1 HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 K 4(K 1+) FORMUL 5 GOL 6(C3 H8 O3) FORMUL 9 CL 2(CL 1-) FORMUL 10 PO4 O4 P 3- FORMUL 16 HOH *396(H2 O) HELIX 1 1 CYS A 20 GLY A 35 1 16 HELIX 2 2 ASN A 52 ASP A 68 1 17 HELIX 3 3 ALA A 81 ARG A 91 1 11 HELIX 4 4 SER A 111 HIS A 125 1 15 HELIX 5 5 VAL A 135 GLY A 140 1 6 HELIX 6 6 LEU A 144 ALA A 152 1 9 HELIX 7 7 THR A 168 GLU A 175 1 8 HELIX 8 8 ASP A 187 ALA A 189 5 3 HELIX 9 9 SER A 190 LEU A 197 1 8 HELIX 10 10 VAL A 205 VAL A 209 5 5 HELIX 11 11 ALA A 210 GLY A 224 1 15 HELIX 12 12 HIS A 225 LEU A 243 1 19 HELIX 13 13 PRO A 249 LEU A 259 1 11 HELIX 14 14 THR A 275 ALA A 289 1 15 HELIX 15 15 CYS B 20 GLY B 35 1 16 HELIX 16 16 GLY B 43 LEU B 51 5 9 HELIX 17 17 ASN B 52 ASP B 68 1 17 HELIX 18 18 ALA B 81 ASN B 93 1 13 HELIX 19 19 SER B 111 HIS B 125 1 15 HELIX 20 20 VAL B 135 GLY B 140 1 6 HELIX 21 21 LEU B 144 ALA B 152 1 9 HELIX 22 22 THR B 168 GLU B 175 1 8 HELIX 23 23 ASP B 187 ALA B 189 5 3 HELIX 24 24 SER B 190 LEU B 197 1 8 HELIX 25 25 VAL B 205 VAL B 209 5 5 HELIX 26 26 ALA B 210 GLU B 223 1 14 HELIX 27 27 HIS B 225 LEU B 243 1 19 HELIX 28 28 PRO B 249 LEU B 259 1 11 HELIX 29 29 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 GLU A 162 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 THR B 102 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 294 1555 1555 2.91 LINK O ALA A 49 K K A 294 1555 1555 3.21 LINK O LEU A 51 K K A 294 1555 1555 2.73 LINK O ALA A 152 K K A 293 1555 1555 2.80 LINK O VAL A 154 K K A 293 1555 1555 2.77 LINK O LYS A 155 K K A 293 1555 1555 3.26 LINK O ILE A 157 K K A 293 1555 1555 2.80 LINK K K A 293 O HOH A 428 1555 1555 2.86 LINK K K A 294 O3 AGOL A 295 1555 1555 2.91 LINK K K A 294 O3 BGOL A 295 1555 1555 3.07 LINK K K A 294 O HOH A 440 1555 1555 3.06 LINK K K A 294 O HOH A 469 1555 1555 3.01 LINK O ALA B 123 K K B 294 1555 1555 2.86 LINK O GLU B 124 K K B 294 1555 1555 3.36 LINK O THR B 126 K K B 294 1555 1555 2.70 LINK O ALA B 152 K K B 293 1555 1555 2.75 LINK O VAL B 154 K K B 293 1555 1555 2.71 LINK O LYS B 155 K K B 293 1555 1555 3.12 LINK O ILE B 157 K K B 293 1555 1555 2.68 LINK K K B 294 O HOH B 343 1555 1555 2.82 LINK K K B 294 O HOH B 378 1555 1555 3.01 LINK K K B 294 O HOH B 438 1555 1555 2.81 CISPEP 1 ASN A 248 PRO A 249 0 7.40 CISPEP 2 LEU A 269 PRO A 270 0 9.77 CISPEP 3 ASN B 248 PRO B 249 0 5.24 CISPEP 4 LEU B 269 PRO B 270 0 9.87 SITE 1 AC1 5 ALA A 152 VAL A 154 LYS A 155 ILE A 157 SITE 2 AC1 5 HOH A 428 SITE 1 AC2 6 SER A 48 ALA A 49 LEU A 51 GOL A 295 SITE 2 AC2 6 HOH A 440 HOH A 469 SITE 1 AC3 14 ALA A 49 ASN A 80 TYR A 106 K A 294 SITE 2 AC3 14 GOL A 298 HOH A 362 HOH A 398 HOH A 429 SITE 3 AC3 14 HOH A 440 HOH A 469 ASN B 80 TYR B 106 SITE 4 AC3 14 GOL B 295 HOH B 380 SITE 1 AC4 3 SER A 111 GLN A 112 HOH A 443 SITE 1 AC5 3 ARG A 109 HOH A 360 HOH A 385 SITE 1 AC6 8 SER A 48 ALA A 49 GLY A 78 TYR A 106 SITE 2 AC6 8 GOL A 295 HOH A 422 ASN B 80 TYR B 107 SITE 1 AC7 3 ALA A 8 THR A 45 ARG A 161 SITE 1 AC8 2 ARG A 21 LYS A 25 SITE 1 AC9 4 ALA B 152 VAL B 154 LYS B 155 ILE B 157 SITE 1 BC1 6 ALA B 123 GLU B 124 THR B 126 HOH B 343 SITE 2 BC1 6 HOH B 378 HOH B 438 SITE 1 BC2 7 ASN A 80 GOL A 295 SER B 48 ALA B 49 SITE 2 BC2 7 GLY B 78 TYR B 106 HOH B 380 SITE 1 BC3 2 SER A 137 ARG B 109 SITE 1 BC4 4 ALA B 8 THR B 44 THR B 45 ARG B 161 CRYST1 121.435 121.435 111.037 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 0.008235 0.004754 0.000000 0.00000 SCALE2 0.000000 0.009509 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009006 0.00000