HEADER LYASE 10-JUN-08 3DEN TITLE STRUCTURE OF E. COLI DHDPS MUTANT Y107W COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DHDPS; COMPND 5 EC: 4.2.1.52; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: DAPA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PBLUESCRIPT; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJG001 KEYWDS DIHYDRODIPICOLINATE SYNTHASE, MONOMER, QUATERNARY STRUCTURE, AMINO- KEYWDS 2 ACID BIOSYNTHESIS, DIAMINOPIMELATE BIOSYNTHESIS, LYASE, LYSINE KEYWDS 3 BIOSYNTHESIS, SCHIFF BASE EXPDTA X-RAY DIFFRACTION AUTHOR F.G.PEARCE,J.A.GERRARD,M.A.PERUGINI,G.B.JAMESON REVDAT 5 01-NOV-23 3DEN 1 REMARK REVDAT 4 10-NOV-21 3DEN 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3DEN 1 VERSN REVDAT 2 24-FEB-09 3DEN 1 VERSN REVDAT 1 25-NOV-08 3DEN 0 JRNL AUTH F.G.PEARCE,R.C.J.DOBSON,A.WEBER,L.A.LANE,M.G.MCCAMMON, JRNL AUTH 2 M.A.SQUIRE,M.A.PERUGINI,G.B.JAMESON,C.V.ROBINSON,J.A.GERRARD JRNL TITL MUTATING THE TIGHT-DIMER INTERFACE OF DIHYDRODIPICOLINATE JRNL TITL 2 SYNTHASE DISRUPTS THE ENZYME QUATERNARY STRUCTURE: TOWARD A JRNL TITL 3 MONOMERIC ENZYME JRNL REF BIOCHEMISTRY V. 47 12108 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18937497 JRNL DOI 10.1021/BI801094T REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45136 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2388 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3324 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 185 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4369 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 448 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : -0.13000 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): 0.181 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.178 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.984 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4566 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6230 ; 1.826 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 602 ; 6.491 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;35.822 ;24.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 743 ;15.690 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;17.433 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 741 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3394 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2245 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3141 ; 0.294 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 440 ; 0.184 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 6 ; 0.149 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 50 ; 0.182 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.078 ; 0.200 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): 2939 ; 0.892 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4750 ; 1.647 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1635 ; 2.873 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1473 ; 4.560 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 292 5 REMARK 3 1 B 1 B 292 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1159 ; 0.12 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 981 ; 0.33 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1159 ; 2.25 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 981 ; 3.17 ; 10.00 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 3DEN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047943. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL 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 : 63201 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 39.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.990 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.98 REMARK 200 R MERGE FOR SHELL (I) : 0.43200 REMARK 200 R SYM FOR SHELL (I) : NULL 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: PDB ENTRY 1YXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M K2HPO4, 6% (W/V) N-OCTYL-BETA-R REMARK 280 -GLUCOPYRANOSIDE , PH 10, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 284K 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 36.85500 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 73.71000 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 73.71000 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 36.85500 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: 10170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 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 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 16 CE NZ REMARK 470 GLU A 124 CD OE1 OE2 REMARK 470 LYS A 155 CD CE NZ REMARK 470 LYS A 257 CE NZ REMARK 470 ARG A 279 NE CZ NH1 NH2 REMARK 470 LYS A 287 CE NZ REMARK 470 LYS B 120 NZ REMARK 470 LYS B 153 NZ REMARK 470 LYS B 155 CG CD CE NZ REMARK 470 GLU B 175 OE1 OE2 REMARK 470 LYS B 219 CE NZ REMARK 470 LYS B 287 CG CD CE NZ REMARK 470 LEU B 292 CG CD1 CD2 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 O3 GOL A 2647 O HOH A 312 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 64 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 ASP A 187 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 213 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 21 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TRP A 107 -65.18 83.23 REMARK 500 TRP A 107 -37.32 79.86 REMARK 500 TRP B 107 -66.02 84.93 REMARK 500 TRP B 107 -44.65 85.23 REMARK 500 ALA B 210 51.98 -145.28 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 293 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 152 O REMARK 620 2 VAL A 154 O 82.1 REMARK 620 3 ILE A 157 O 99.8 83.8 REMARK 620 N 1 2 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 83.4 REMARK 620 3 ILE B 157 O 97.6 86.1 REMARK 620 N 1 2 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 GOL 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 PO4 A 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A2647 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 295 DBREF 3DEN A 1 292 UNP P0A6L2 DAPA_ECOLI 1 292 DBREF 3DEN B 1 292 UNP P0A6L2 DAPA_ECOLI 1 292 SEQADV 3DEN TRP A 107 UNP P0A6L2 TYR 107 ENGINEERED MUTATION SEQADV 3DEN TRP B 107 UNP P0A6L2 TYR 107 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 TRP 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 KGC 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 TRP 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 KGC 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 MODRES 3DEN KGC A 161 LYS MODRES 3DEN KGC B 161 LYS HET KGC A 161 18 HET KGC B 161 18 HET K A 293 1 HET GOL A 294 6 HET GOL A 295 6 HET PO4 A 296 5 HET GOL A2647 6 HET K B 293 1 HET PO4 B 294 5 HET PO4 B 295 5 HETNAM KGC N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L- HETNAM 2 KGC LYSINE HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 KGC 2(C11 H18 N2 O6) FORMUL 3 K 2(K 1+) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 6 PO4 3(O4 P 3-) FORMUL 11 HOH *448(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 LYS A 153 1 10 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 GLU B 47 LEU B 51 5 5 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 ALA B 152 1 9 HELIX 23 23 THR B 168 GLU B 175 1 8 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 SER A 41 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 TYR A 133 1 O ILE A 131 N CYS A 100 SHEET 6 A 9 ILE A 157 ILE A 160 1 O GLY A 159 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 TYR B 133 1 O ILE B 131 N THR B 102 SHEET 6 B 9 ILE B 157 ILE B 160 1 O GLY B 159 N LEU B 132 SHEET 7 B 9 VAL B 182 SER B 185 1 O LEU B 184 N ILE B 160 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 C ILE A 160 N KGC A 161 1555 1555 1.35 LINK C KGC A 161 N GLU A 162 1555 1555 1.34 LINK C ILE B 160 N KGC B 161 1555 1555 1.35 LINK C KGC B 161 N GLU B 162 1555 1555 1.33 LINK O ALA A 152 K K A 293 1555 1555 2.63 LINK O VAL A 154 K K A 293 1555 1555 2.62 LINK O ILE A 157 K K A 293 1555 1555 2.65 LINK O ALA B 152 K K B 293 1555 1555 2.77 LINK O VAL B 154 K K B 293 1555 1555 2.56 LINK O ILE B 157 K K B 293 1555 1555 2.73 CISPEP 1 ASN A 248 PRO A 249 0 8.87 CISPEP 2 LEU A 269 PRO A 270 0 9.09 CISPEP 3 ASN B 248 PRO B 249 0 5.53 CISPEP 4 LEU B 269 PRO B 270 0 11.14 SITE 1 AC1 5 ALA A 152 VAL A 154 LYS A 155 ILE A 157 SITE 2 AC1 5 HOH A 501 SITE 1 AC2 4 ASP A 29 ALA A 33 HIS A 125 GOL A 295 SITE 1 AC3 4 LYS A 26 TYR A 30 HIS A 125 GOL A 294 SITE 1 AC4 1 ARG A 109 SITE 1 AC5 9 ALA A 81 GLU A 84 HOH A 312 HOH A 439 SITE 2 AC5 9 HOH A 440 ALA B 49 THR B 50 LEU B 51 SITE 3 AC5 9 ASN B 52 SITE 1 AC6 4 ALA B 152 VAL B 154 LYS B 155 ILE B 157 SITE 1 AC7 4 HOH A 523 ARG B 21 LYS B 25 HOH B 356 SITE 1 AC8 5 TYR B 116 LYS B 120 ARG B 150 HOH B 432 SITE 2 AC8 5 HOH B 449 CRYST1 121.196 121.196 110.565 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 0.008251 0.004764 0.000000 0.00000 SCALE2 0.000000 0.009528 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009044 0.00000