HEADER LYASE 30-NOV-07 3BI8 OBSLTE 22-SEP-09 3BI8 3IRD TITLE STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM CLOSTRIDIUM TITLE 2 BOTULINUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.2.1.52; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM BOTULINUM; SOURCE 3 ORGANISM_TAXID: 1491; SOURCE 4 GENE: DAPA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS TIM-BARREL, DIHYDRODIPICOLINATE SYNTHASE, AMINO-ACID KEYWDS 2 BIOSYNTHESIS, CYTOPLASM, DIAMINOPIMELATE BIOSYNTHESIS, KEYWDS 3 LYASE, LYSINE BIOSYNTHESIS, SCHIFF BASE EXPDTA X-RAY DIFFRACTION AUTHOR S.C.ATKINSON,R.C.J.DOBSON,M.GORMAN,M.PARKER,M.A.PERUGINI REVDAT 2 22-SEP-09 3BI8 1 OBSLTE REVDAT 1 02-DEC-08 3BI8 0 JRNL AUTH S.C.ATKINSON,R.C.J.DOBSON,M.GORMAN,M.PARKER, JRNL AUTH 2 M.A.PERUGINI JRNL TITL STRUCTURE OF DHDPS FROM CLOSTRIDIUM BOTULINUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 75.1 REMARK 3 NUMBER OF REFLECTIONS : 13974 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) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 744 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) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 169 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 12.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 4 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2224 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 307 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.88000 REMARK 3 B22 (A**2) : 0.88000 REMARK 3 B33 (A**2) : -1.75000 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): 0.253 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.177 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.461 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2287 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3098 ; 1.487 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 296 ; 6.302 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;39.802 ;26.951 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 428 ;13.175 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;15.347 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 380 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1628 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1163 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1611 ; 0.294 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 223 ; 0.157 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.092 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 67 ; 0.179 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 47 ; 0.217 ; 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): 1454 ; 0.549 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2371 ; 1.054 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 849 ; 2.129 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 724 ; 3.624 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 3BI8 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-DEC-07. REMARK 100 THE RCSB ID CODE IS RCSB045553. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5.66 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 : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14754 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 36.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 74.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 18.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.17200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 1O5K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POLYETHYLENE GLYCOL 3350, MALIC REMARK 280 ACID (PH 5.66), TRIS-HCL (PH 8.0), VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z 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 0.000000 -1.000000 0.000000 46.44900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 46.44900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.18300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 46.44900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 46.44900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.18300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 46.44900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.44900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.18300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 46.44900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.44900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.18300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: DETAILS: AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN 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: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -111.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -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 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 -60.36600 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -60.36600 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -60.36600 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -60.36600 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 297 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 298 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 549 O HOH A 568 4554 2.04 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 TYR A 108 -69.92 77.09 REMARK 500 LYS A 110 -161.46 57.06 REMARK 500 THR A 111 -175.98 178.91 REMARK 500 THR A 248 111.41 -37.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 544 DISTANCE = 5.38 ANGSTROMS REMARK 525 HOH A 568 DISTANCE = 5.60 ANGSTROMS 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 293 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 153 O REMARK 620 2 ASP A 155 O 99.7 REMARK 620 3 ILE A 158 O 106.3 101.8 REMARK 620 4 HOH A 402 O 136.5 85.5 114.8 REMARK 620 5 HOH A 363 O 81.2 161.9 95.1 81.8 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 MLT A 1 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 293 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 294 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 295 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 296 DBREF 3BI8 A 2 292 UNP A7FYA1 A7FYA1_CLOB1 2 292 SEQRES 1 A 291 SER ILE PHE LYS GLY SER GLY VAL ALA ILE ILE THR PRO SEQRES 2 A 291 PHE THR ASN THR GLY VAL ASP PHE ASP LYS LEU SER GLU SEQRES 3 A 291 LEU ILE GLU TRP HIS ILE LYS SER LYS THR ASP ALA ILE SEQRES 4 A 291 ILE VAL CYS GLY THR THR GLY GLU ALA THR THR MET THR SEQRES 5 A 291 GLU THR GLU ARG LYS GLU THR ILE LYS PHE VAL ILE ASP SEQRES 6 A 291 LYS VAL ASN LYS ARG ILE PRO VAL ILE ALA GLY THR GLY SEQRES 7 A 291 SER ASN ASN THR ALA ALA SER ILE ALA MET SER LYS TRP SEQRES 8 A 291 ALA GLU SER ILE GLY VAL ASP GLY LEU LEU VAL ILE THR SEQRES 9 A 291 PRO TYR TYR ASN LYS THR THR GLN LYS GLY LEU VAL LYS SEQRES 10 A 291 HIS PHE LYS ALA VAL SER ASP ALA VAL SER THR PRO ILE SEQRES 11 A 291 ILE ILE TYR ASN VAL PRO GLY ARG THR GLY LEU ASN ILE SEQRES 12 A 291 THR PRO GLY THR LEU LYS GLU LEU CYS GLU ASP LYS ASN SEQRES 13 A 291 ILE VAL ALA VAL LYS GLU ALA SER GLY ASN ILE SER GLN SEQRES 14 A 291 ILE ALA GLN ILE LYS ALA LEU CYS GLY ASP LYS LEU ASP SEQRES 15 A 291 ILE TYR SER GLY ASN ASP ASP GLN ILE ILE PRO ILE LEU SEQRES 16 A 291 ALA LEU GLY GLY ILE GLY VAL ILE SER VAL LEU ALA ASN SEQRES 17 A 291 VAL ILE PRO GLU ASP VAL HIS ASN MET CYS GLU LEU TYR SEQRES 18 A 291 LEU ASN GLY LYS VAL ASN GLU ALA LEU LYS ILE GLN LEU SEQRES 19 A 291 ASP SER LEU ALA LEU THR ASN ALA LEU PHE ILE GLU THR SEQRES 20 A 291 ASN PRO ILE PRO VAL LYS THR ALA MET ASN LEU MET ASN SEQRES 21 A 291 MET LYS VAL GLY ASP LEU ARG LEU PRO LEU CYS GLU MET SEQRES 22 A 291 ASN GLU ASN ASN LEU GLU ILE LEU LYS LYS GLU LEU LYS SEQRES 23 A 291 ALA TYR ASN LEU MET HET MLT A 1 18 HET NA A 293 1 HET GOL A 294 6 HET GOL A 295 6 HET GOL A 296 6 HETNAM MLT MALATE ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL FORMUL 2 MLT C4 H5 O5 1- FORMUL 3 NA NA 1+ FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 HOH *289(H2 O) HELIX 1 1 ASP A 21 SER A 35 1 15 HELIX 2 2 GLY A 44 MET A 52 5 9 HELIX 3 3 THR A 53 ASN A 69 1 17 HELIX 4 4 ASN A 82 ILE A 96 1 15 HELIX 5 5 THR A 112 ALA A 126 1 15 HELIX 6 6 VAL A 136 GLY A 141 1 6 HELIX 7 7 THR A 145 CYS A 153 1 9 HELIX 8 8 ASN A 167 GLY A 179 1 13 HELIX 9 9 ASP A 180 LEU A 182 5 3 HELIX 10 10 ASN A 188 ASP A 190 5 3 HELIX 11 11 GLN A 191 LEU A 198 1 8 HELIX 12 12 VAL A 206 VAL A 210 5 5 HELIX 13 13 ILE A 211 ASN A 224 1 14 HELIX 14 14 LYS A 226 SER A 237 1 12 HELIX 15 15 SER A 237 LEU A 244 1 8 HELIX 16 16 PRO A 250 MET A 260 1 11 HELIX 17 17 ASN A 275 TYR A 289 1 15 SHEET 1 A 9 GLY A 6 ALA A 10 0 SHEET 2 A 9 ALA A 39 VAL A 42 1 O ILE A 41 N VAL A 9 SHEET 3 A 9 VAL A 74 GLY A 77 1 O ILE A 75 N VAL A 42 SHEET 4 A 9 GLY A 100 ILE A 104 1 O LEU A 102 N ALA A 76 SHEET 5 A 9 ILE A 131 ASN A 135 1 O ILE A 132 N LEU A 101 SHEET 6 A 9 ILE A 158 GLU A 163 1 O LYS A 162 N ILE A 133 SHEET 7 A 9 ASP A 183 SER A 186 1 O TYR A 185 N VAL A 161 SHEET 8 A 9 GLY A 202 SER A 205 1 O GLY A 202 N SER A 186 SHEET 9 A 9 GLY A 6 ALA A 10 1 N ALA A 10 O SER A 205 LINK O CYS A 153 NA NA A 293 1555 1555 2.38 LINK O ASP A 155 NA NA A 293 1555 1555 2.24 LINK O ILE A 158 NA NA A 293 1555 1555 2.30 LINK NA NA A 293 O HOH A 402 1555 1555 2.39 LINK NA NA A 293 O HOH A 363 1555 1555 2.39 CISPEP 1 ASN A 249 PRO A 250 0 0.41 CISPEP 2 LEU A 269 PRO A 270 0 10.78 SITE 1 AC1 15 ALA A 10 GLY A 44 THR A 45 THR A 46 SITE 2 AC1 15 LEU A 102 TYR A 134 ARG A 139 LYS A 162 SITE 3 AC1 15 VAL A 206 PHE A 245 ASN A 249 HOH A 492 SITE 4 AC1 15 HOH A 524 HOH A 556 HOH A 583 SITE 1 AC2 5 CYS A 153 ASP A 155 ILE A 158 HOH A 363 SITE 2 AC2 5 HOH A 402 SITE 1 AC3 6 ASN A 258 ASP A 266 LEU A 267 HOH A 331 SITE 2 AC3 6 HOH A 471 HOH A 539 SITE 1 AC4 6 SER A 95 MET A 260 LEU A 291 HOH A 359 SITE 2 AC4 6 HOH A 377 HOH A 504 SITE 1 AC5 6 LYS A 36 ASP A 125 HIS A 216 ASN A 217 SITE 2 AC5 6 GLU A 220 HOH A 581 CRYST1 92.898 92.898 60.366 90.00 90.00 90.00 P 42 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010764 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010764 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016566 0.00000