10 20 30 40 50 60 70 80 1T6M - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LYASE 06-MAY-04 1T6M
TITLE X-RAY STRUCTURE OF THE R70D PI-PLC ENZYME: INSIGHT INTO THE TITLE 2 ROLE OF CALCIUM AND SURROUNDING AMINO ACIDS ON ACTIVE SITE TITLE 3 GEOMETRY AND CATALYSIS.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1-PHOSPHATIDYLINOSITOL PHOSPHODIESTERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHATIDYLINOSITOL DIACYLGLYCEROL-LYASE, COMPND 5 PHOSPHATIDYLINOSITOL- SPECIFIC PHOSPHOLIPASE C, PI-PLC; COMPND 6 EC: 4.6.1.13; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS THURINGIENSIS; SOURCE 3 ORGANISM_TAXID: 1428; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PI-PLC, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.APIYO,L.ZHAO,M.-D.TSAI,T.L.SELBY
REVDAT 2 24-FEB-09 1T6M 1 VERSN REVDAT 1 16-AUG-05 1T6M 0
JRNL AUTH D.APIYO,L.ZHAO,M.-D.TSAI,T.L.SELBY JRNL TITL X-RAY STRUCTURE OF THE R69D JRNL TITL 2 PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C JRNL TITL 3 ENZYME: INSIGHT INTO THE ROLE OF CALCIUM AND JRNL TITL 4 SURROUNDING AMINO ACIDS IN ACTIVE SITE GEOMETRY JRNL TITL 5 AND CATALYSIS. JRNL REF BIOCHEMISTRY V. 44 9980 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 16042375 JRNL DOI 10.1021/BI047896V
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN
REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.9999 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 36951 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3711 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) : 2.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2405 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 263 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4836 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 228 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.99900 REMARK 3 B22 (A**2) : 1.95200 REMARK 3 B33 (A**2) : 1.04700 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): 0.276 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.233 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.147 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.346 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.871 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4875 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4066 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6635 ; 1.546 ; 1.922 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9499 ; 0.957 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 583 ; 7.613 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 255 ;39.152 ;25.373 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 797 ;16.664 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ; 7.699 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 708 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5471 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 979 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1286 ; 0.258 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4303 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2642 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 463 ; 0.290 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.517 ; 0.200 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): 31 ; 0.262 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 64 ; 0.264 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 38 ; 0.319 ; 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): 3014 ; 0.840 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1183 ; 0.158 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4758 ; 1.397 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2212 ; 2.023 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1877 ; 3.062 ; 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 : BABINET MODEL WITH 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 1T6M COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-04. REMARK 100 THE RCSB ID CODE IS RCSB022377.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37903 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.107 REMARK 200 RESOLUTION RANGE LOW (A) : 43.437 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: XTALVIEW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG-3000, 0.2M NH4CL, 20 MM REMARK 280 CHES BUFFER, PH 9.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 48.28100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.28100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 45.61050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 73.86250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.61050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 73.86250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.28100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.61050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 73.86250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.28100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.61050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 73.86250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 4 REMARK 465 LYS A 301 REMARK 465 GLU A 302 REMARK 465 MET B 4 REMARK 465 LYS B 301 REMARK 465 GLU B 302
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 OE1 GLU A 186 OD2 ASP B 228 6554 2.11 REMARK 500 OE2 GLU A 221 NZ LYS B 213 6554 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 282 CB GLU A 282 CG 0.888 REMARK 500 GLU B 282 CD GLU B 282 OE1 0.067 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 ASN A 13 CA - C - N ANGL. DEV. = 14.3 DEGREES REMARK 500 VAL A 198 CB - CA - C ANGL. DEV. = -11.6 DEGREES REMARK 500 LEU A 232 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 TYR B 92 C - N - CA ANGL. DEV. = -15.9 DEGREES REMARK 500 PRO B 286 C - N - CA ANGL. DEV. = -13.0 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 LYS A 16 19.42 -141.65 REMARK 500 TYR A 92 46.60 -108.93 REMARK 500 GLU A 129 -74.54 -66.47 REMARK 500 TYR A 140 -54.50 -121.20 REMARK 500 GLU A 150 -142.46 -131.03 REMARK 500 TRP A 182 74.50 78.14 REMARK 500 LYS A 205 65.55 79.58 REMARK 500 THR A 244 175.98 43.81 REMARK 500 ALA A 245 -172.20 -64.30 REMARK 500 TRP A 246 -15.52 75.98 REMARK 500 ASN A 247 38.88 -145.48 REMARK 500 ASN A 281 -178.55 -170.02 REMARK 500 LYS B 16 27.21 -141.47 REMARK 500 ASP B 37 57.69 39.36 REMARK 500 TYR B 140 -57.32 -128.47 REMARK 500 GLU B 150 -134.11 -139.50 REMARK 500 TYR B 181 -72.04 -28.63 REMARK 500 TRP B 182 65.12 71.87 REMARK 500 THR B 244 87.81 -27.30 REMARK 500 ALA B 245 -155.78 170.50 REMARK 500 TRP B 246 46.29 -101.53 REMARK 500 ASN B 247 35.70 -154.69 REMARK 500 SER B 285 -71.07 -70.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 284 SER A 285 -128.47 REMARK 500 SER A 285 PRO A 286 148.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 186 10.97 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 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 546 O REMARK 620 2 ASP A 228 OD2 110.1 REMARK 620 3 HIS A 231 NE2 99.5 119.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 73 OD1 REMARK 620 2 ASP A 37 OD2 82.3 REMARK 620 3 HOH A 549 O 99.9 143.6 REMARK 620 4 HOH A 503 O 138.4 84.1 70.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 37 OD1 REMARK 620 2 ASP B 73 OD2 90.5 REMARK 620 3 ASP B 37 OD2 38.9 112.7 REMARK 620 4 HOH B 509 O 86.3 169.4 70.4 REMARK 620 5 HOH B 554 O 159.7 96.3 121.4 90.1 REMARK 620 6 ASP B 73 OD1 100.2 39.1 137.3 131.8 97.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 230 OD1 REMARK 620 2 ASP B 228 OD2 119.3 REMARK 620 3 ASP B 228 OD1 88.2 39.2 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 CA A 501 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 502 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 503 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 504
DBREF 1T6M A 5 302 UNP P08954 PLC_BACTU 32 329 DBREF 1T6M B 5 302 UNP P08954 PLC_BACTU 32 329
SEQADV 1T6M MET A 4 UNP P08954 INITIATING METHIONINE SEQADV 1T6M ASP A 73 UNP P08954 ARG 100 ENGINEERED SEQADV 1T6M MET B 4 UNP P08954 INITIATING METHIONINE SEQADV 1T6M ASP B 73 UNP P08954 ARG 100 ENGINEERED
SEQRES 1 A 299 MET ALA SER SER VAL ASN GLU LEU GLU ASN TRP SER LYS SEQRES 2 A 299 TRP MET GLN PRO ILE PRO ASP ASN ILE PRO LEU ALA ARG SEQRES 3 A 299 ILE SER ILE PRO GLY THR HIS ASP SER GLY THR PHE LYS SEQRES 4 A 299 LEU GLN ASN PRO ILE LYS GLN VAL TRP GLY MET THR GLN SEQRES 5 A 299 GLU TYR ASP PHE ARG TYR GLN MET ASP HIS GLY ALA ARG SEQRES 6 A 299 ILE PHE ASP ILE ASP GLY ARG LEU THR ASP ASP ASN THR SEQRES 7 A 299 ILE VAL LEU HIS HIS GLY PRO LEU TYR LEU TYR VAL THR SEQRES 8 A 299 LEU HIS GLU PHE ILE ASN GLU ALA LYS GLN PHE LEU LYS SEQRES 9 A 299 ASP ASN PRO SER GLU THR ILE ILE MET SER LEU LYS LYS SEQRES 10 A 299 GLU TYR GLU ASP MET LYS GLY ALA GLU GLY SER PHE SER SEQRES 11 A 299 SER THR PHE GLU LYS ASN TYR PHE VAL ASP PRO ILE PHE SEQRES 12 A 299 LEU LYS THR GLU GLY ASN ILE LYS LEU GLY ASP ALA ARG SEQRES 13 A 299 GLY LYS ILE VAL LEU LEU LYS ARG TYR SER GLY SER ASN SEQRES 14 A 299 GLU SER GLY GLY TYR ASN ASN PHE TYR TRP PRO ASP ASN SEQRES 15 A 299 GLU THR PHE THR THR THR VAL ASN GLN ASN VAL ASN VAL SEQRES 16 A 299 THR VAL GLN ASP LYS TYR LYS VAL ASN TYR ASP GLU LYS SEQRES 17 A 299 VAL LYS SER ILE LYS ASP THR MET ASP GLU THR MET ASN SEQRES 18 A 299 ASN SER GLU ASP LEU ASN HIS LEU TYR ILE ASN PHE THR SEQRES 19 A 299 SER LEU SER SER GLY GLY THR ALA TRP ASN SER PRO TYR SEQRES 20 A 299 TYR TYR ALA SER TYR ILE ASN PRO GLU ILE ALA ASN ASP SEQRES 21 A 299 ILE LYS GLN LYS ASN PRO THR ARG VAL GLY TRP VAL ILE SEQRES 22 A 299 GLN ASP TYR ILE ASN GLU LYS TRP SER PRO LEU LEU TYR SEQRES 23 A 299 GLN GLU VAL ILE ARG ALA ASN LYS SER LEU ILE LYS GLU SEQRES 1 B 299 MET ALA SER SER VAL ASN GLU LEU GLU ASN TRP SER LYS SEQRES 2 B 299 TRP MET GLN PRO ILE PRO ASP ASN ILE PRO LEU ALA ARG SEQRES 3 B 299 ILE SER ILE PRO GLY THR HIS ASP SER GLY THR PHE LYS SEQRES 4 B 299 LEU GLN ASN PRO ILE LYS GLN VAL TRP GLY MET THR GLN SEQRES 5 B 299 GLU TYR ASP PHE ARG TYR GLN MET ASP HIS GLY ALA ARG SEQRES 6 B 299 ILE PHE ASP ILE ASP GLY ARG LEU THR ASP ASP ASN THR SEQRES 7 B 299 ILE VAL LEU HIS HIS GLY PRO LEU TYR LEU TYR VAL THR SEQRES 8 B 299 LEU HIS GLU PHE ILE ASN GLU ALA LYS GLN PHE LEU LYS SEQRES 9 B 299 ASP ASN PRO SER GLU THR ILE ILE MET SER LEU LYS LYS SEQRES 10 B 299 GLU TYR GLU ASP MET LYS GLY ALA GLU GLY SER PHE SER SEQRES 11 B 299 SER THR PHE GLU LYS ASN TYR PHE VAL ASP PRO ILE PHE SEQRES 12 B 299 LEU LYS THR GLU GLY ASN ILE LYS LEU GLY ASP ALA ARG SEQRES 13 B 299 GLY LYS ILE VAL LEU LEU LYS ARG TYR SER GLY SER ASN SEQRES 14 B 299 GLU SER GLY GLY TYR ASN ASN PHE TYR TRP PRO ASP ASN SEQRES 15 B 299 GLU THR PHE THR THR THR VAL ASN GLN ASN VAL ASN VAL SEQRES 16 B 299 THR VAL GLN ASP LYS TYR LYS VAL ASN TYR ASP GLU LYS SEQRES 17 B 299 VAL LYS SER ILE LYS ASP THR MET ASP GLU THR MET ASN SEQRES 18 B 299 ASN SER GLU ASP LEU ASN HIS LEU TYR ILE ASN PHE THR SEQRES 19 B 299 SER LEU SER SER GLY GLY THR ALA TRP ASN SER PRO TYR SEQRES 20 B 299 TYR TYR ALA SER TYR ILE ASN PRO GLU ILE ALA ASN ASP SEQRES 21 B 299 ILE LYS GLN LYS ASN PRO THR ARG VAL GLY TRP VAL ILE SEQRES 22 B 299 GLN ASP TYR ILE ASN GLU LYS TRP SER PRO LEU LEU TYR SEQRES 23 B 299 GLN GLU VAL ILE ARG ALA ASN LYS SER LEU ILE LYS GLU
HET CA A 501 1 HET CA A 502 1 HET CA B 503 1 HET CA B 504 1
HETNAM CA CALCIUM ION
FORMUL 3 CA 4(CA 2+) FORMUL 7 HOH *228(H2 O)
HELIX 1 1 SER A 7 ASN A 13 5 7 HELIX 2 2 GLY A 39 LEU A 43 5 5 HELIX 3 3 ASN A 45 MET A 53 1 9 HELIX 4 4 ASP A 58 HIS A 65 1 8 HELIX 5 5 LEU A 95 ASN A 109 1 15 HELIX 6 6 SER A 131 TYR A 140 1 10 HELIX 7 7 LYS A 154 ARG A 159 1 6 HELIX 8 8 ASN A 207 ASN A 225 1 19 HELIX 9 9 SER A 248 ASN A 268 1 21 HELIX 10 10 LEU A 287 ALA A 295 1 9 HELIX 11 11 ASN A 296 ILE A 300 5 5 HELIX 12 12 SER B 7 ASN B 13 5 7 HELIX 13 13 PRO B 26 ILE B 30 5 5 HELIX 14 14 ASN B 45 MET B 53 1 9 HELIX 15 15 ASP B 58 HIS B 65 1 8 HELIX 16 16 LEU B 95 ASN B 109 1 15 HELIX 17 17 SER B 131 TYR B 140 1 10 HELIX 18 18 LYS B 154 ARG B 159 1 6 HELIX 19 19 ASN B 207 ASN B 225 1 19 HELIX 20 20 SER B 248 ASN B 268 1 21 HELIX 21 21 LEU B 287 ALA B 295 1 9 HELIX 22 22 ASN B 296 ILE B 300 5 5
SHEET 1 A 5 LEU A 89 THR A 94 0 SHEET 2 A 5 ILE A 82 HIS A 86 -1 N LEU A 84 O VAL A 93 SHEET 3 A 5 ILE A 69 LEU A 76 -1 N ARG A 75 O VAL A 83 SHEET 4 A 5 ILE A 114 LYS A 120 1 O SER A 117 N PHE A 70 SHEET 5 A 5 ILE A 162 ARG A 167 1 O VAL A 163 N ILE A 114 SHEET 1 B 8 LEU A 89 THR A 94 0 SHEET 2 B 8 ILE A 82 HIS A 86 -1 N LEU A 84 O VAL A 93 SHEET 3 B 8 ILE A 69 LEU A 76 -1 N ARG A 75 O VAL A 83 SHEET 4 B 8 ILE A 32 THR A 35 1 N THR A 35 O ILE A 69 SHEET 5 B 8 TRP A 274 GLN A 277 1 O VAL A 275 N GLY A 34 SHEET 6 B 8 HIS A 231 PHE A 236 1 N TYR A 233 O TRP A 274 SHEET 7 B 8 VAL A 196 GLN A 201 1 N ASN A 197 O LEU A 232 SHEET 8 B 8 THR A 187 ASN A 193 -1 N VAL A 192 O VAL A 196 SHEET 1 C 5 LEU B 89 THR B 94 0 SHEET 2 C 5 ILE B 82 HIS B 86 -1 N LEU B 84 O VAL B 93 SHEET 3 C 5 ILE B 69 LEU B 76 -1 N ARG B 75 O VAL B 83 SHEET 4 C 5 ILE B 114 LYS B 120 1 O LYS B 119 N GLY B 74 SHEET 5 C 5 ILE B 162 ARG B 167 1 O LEU B 165 N MET B 116 SHEET 1 D 8 LEU B 89 THR B 94 0 SHEET 2 D 8 ILE B 82 HIS B 86 -1 N LEU B 84 O VAL B 93 SHEET 3 D 8 ILE B 69 LEU B 76 -1 N ARG B 75 O VAL B 83 SHEET 4 D 8 ILE B 32 THR B 35 1 N THR B 35 O ILE B 69 SHEET 5 D 8 TRP B 274 GLN B 277 1 O GLN B 277 N GLY B 34 SHEET 6 D 8 HIS B 231 PHE B 236 1 N ASN B 235 O TRP B 274 SHEET 7 D 8 VAL B 196 GLN B 201 1 N GLN B 201 O ILE B 234 SHEET 8 D 8 THR B 187 ASN B 193 -1 N VAL B 192 O VAL B 196
LINK CA CA A 501 O HOH A 546 1555 1555 2.27 LINK CA CA A 501 OD2 ASP A 228 1555 1555 1.95 LINK CA CA A 501 NE2 HIS A 231 1555 1555 3.15 LINK CA CA A 502 OD1 ASP A 73 1555 1555 2.17 LINK CA CA A 502 OD2 ASP A 37 1555 1555 2.12 LINK CA CA A 502 O HOH A 549 1555 1555 2.91 LINK CA CA A 502 O HOH A 503 1555 1555 2.85 LINK CA CA B 503 OD1 ASP B 37 1555 1555 2.12 LINK CA CA B 503 OD2 ASP B 73 1555 1555 2.05 LINK CA CA B 503 OD2 ASP B 37 1555 1555 3.38 LINK CA CA B 503 O HOH B 509 1555 1555 3.24 LINK CA CA B 503 O HOH B 554 1555 1555 2.98 LINK CA CA B 503 OD1 ASP B 73 1555 1555 3.36 LINK CA CA B 504 OD1 ASN B 230 1555 1555 2.07 LINK CA CA B 504 OD2 ASP B 228 1555 1555 3.37 LINK CA CA B 504 OD1 ASP B 228 1555 1555 2.15
CISPEP 1 ASN A 13 TRP A 14 0 -17.20 CISPEP 2 THR A 244 ALA A 245 0 -5.64
SITE 1 AC1 4 ASP A 228 ASN A 230 HIS A 231 HOH A 546 SITE 1 AC2 4 ASP A 37 ASP A 73 HOH A 503 HOH A 549 SITE 1 AC3 3 ASP B 37 ASP B 73 HOH B 554 SITE 1 AC4 2 ASP B 228 ASN B 230
CRYST1 91.221 147.725 96.562 90.00 90.00 90.00 C 2 2 21 16
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 0.010962 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006769 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010356 0.00000