HEADER HYDROLASE 03-MAY-16 5JP6 TITLE BDELLOVIBRIO BACTERIOVORUS PEPTIDOGLYCAN DEACETYLASE BD3279 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE POLYSACCHARIDE DEACETYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BDELLOVIBRIO BACTERIOVORUS HD100; SOURCE 3 ORGANISM_TAXID: 264462; SOURCE 4 GENE: BD3279; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS PEPTIDOGLYCAN DEACETYLASE CE-4 CARBOHYDRATE ESTERASE 4, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.L.LOVERING REVDAT 6 10-JAN-24 5JP6 1 LINK REVDAT 5 16-OCT-19 5JP6 1 REMARK REVDAT 4 10-JUL-19 5JP6 1 REMARK REVDAT 3 20-FEB-19 5JP6 1 REMARK LINK REVDAT 2 30-AUG-17 5JP6 1 REMARK REVDAT 1 01-JUN-16 5JP6 0 JRNL AUTH C.LAMBERT,T.R.LERNER,N.K.BUI,H.SOMERS,S.AIZAWA,S.LIDDELL, JRNL AUTH 2 A.CLARK,W.VOLLMER,A.L.LOVERING,R.E.SOCKETT JRNL TITL INTERRUPTING PEPTIDOGLYCAN DEACETYLATION DURING BDELLOVIBRIO JRNL TITL 2 PREDATOR-PREY INTERACTION PREVENTS ULTIMATE DESTRUCTION OF JRNL TITL 3 PREY WALL, LIBERATING BACTERIAL-GHOSTS. JRNL REF SCI REP V. 6 26010 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27211869 JRNL DOI 10.1038/SREP26010 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 97.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 86803 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4581 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6216 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 361 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2689 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 265 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.20000 REMARK 3 B12 (A**2) : 0.03000 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): 0.050 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.048 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.880 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2815 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2677 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3809 ; 1.552 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6147 ; 0.863 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 356 ; 5.558 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;34.399 ;23.826 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 504 ;12.687 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;12.221 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 415 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3249 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 691 ; 0.001 ; 0.020 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): 1376 ; 2.825 ; 2.617 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1375 ; 2.787 ; 2.613 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1716 ; 3.398 ; 3.932 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 5492 ; 4.286 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 82 ;34.609 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5616 ;15.856 ; 5.000 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.10 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5JP6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000220992. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91430 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 97.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.1000 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 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: PHASER REMARK 200 STARTING MODEL: 2C1G REMARK 200 REMARK 200 REMARK: DIAMOND REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA CACODYLATE PH 6.5 0.2M MG REMARK 280 ACETATE 20% W/V/ PEG 8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 26.61967 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 53.23933 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 39.92950 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 66.54917 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 13.30983 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 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 1 REMARK 465 TYR A 2 REMARK 465 MET A 3 REMARK 465 LYS A 4 REMARK 465 LYS A 5 REMARK 465 LEU A 6 REMARK 465 VAL A 7 REMARK 465 PHE A 8 REMARK 465 GLY A 9 REMARK 465 GLY A 10 REMARK 465 MET A 11 REMARK 465 LEU A 12 REMARK 465 ILE A 13 REMARK 465 VAL A 14 REMARK 465 SER A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 SER A 18 REMARK 465 LEU A 19 REMARK 465 VAL A 20 REMARK 465 GLY A 21 REMARK 465 CYS A 22 REMARK 465 HIS A 231 REMARK 465 ALA A 232 REMARK 465 CYS A 233 REMARK 465 LEU A 234 REMARK 465 GLY A 235 REMARK 465 THR A 236 REMARK 465 SER A 237 REMARK 465 VAL A 238 REMARK 465 ALA A 239 REMARK 465 CYS A 240 REMARK 465 TYR A 241 REMARK 465 LYS A 242 REMARK 465 GLN A 243 REMARK 465 MET A 244 REMARK 465 GLY A 245 REMARK 465 ASN A 246 REMARK 465 ARG A 247 REMARK 465 ASN A 248 REMARK 465 GLN A 380 REMARK 465 GLN A 381 REMARK 465 LEU A 382 REMARK 465 PRO A 383 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 CB MET A 23 OE2 GLU A 77 1.52 REMARK 500 CG MET A 23 OE2 GLU A 77 1.81 REMARK 500 SD MET A 23 OE2 GLU A 81 1.99 REMARK 500 SD MET A 23 NZ LYS A 80 2.14 REMARK 500 CA MET A 23 OE2 GLU A 77 2.17 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 MET A 155 CG MET A 155 SD -0.173 REMARK 500 GLU A 314 CD GLU A 314 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 ARG A 208 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 208 NE - CZ - NH2 ANGL. DEV. = -7.4 DEGREES REMARK 500 PXU A 279 O - C - N ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG A 329 NE - CZ - NH2 ANGL. DEV. = -3.5 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 CYS A 109 10.35 -145.17 REMARK 500 ASN A 149 84.60 -156.37 REMARK 500 TYR A 159 127.40 -175.18 REMARK 500 ASP A 177 1.96 84.20 REMARK 500 ALA A 300 -147.09 -97.85 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 MET A 23 SER A 24 -148.73 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 ANGLE, 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 PXU A 279 22.85 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 765 DISTANCE = 6.26 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 177 OD2 REMARK 620 2 HIS A 227 NE2 139.8 REMARK 620 3 TYR A 280 OH 107.3 98.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 682 O REMARK 620 2 HOH A 734 O 87.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 DBREF 5JP6 A 1 383 UNP Q6MI90 Q6MI90_BDEBA 1 383 SEQADV 5JP6 MET A 23 UNP Q6MI90 GLY 23 ENGINEERED MUTATION SEQRES 1 A 383 MET TYR MET LYS LYS LEU VAL PHE GLY GLY MET LEU ILE SEQRES 2 A 383 VAL SER ALA ALA SER LEU VAL GLY CYS MET SER GLN ILE SEQRES 3 A 383 GLY SER SER VAL ARG GLN ALA VAL SER ASP ASN GLN SER SEQRES 4 A 383 ALA GLN THR LEU VAL GLU TRP GLU ASN SER GLU ALA ASN SEQRES 5 A 383 PRO GLU ALA LEU PHE ALA ASN TRP ARG HIS GLU PHE MET SEQRES 6 A 383 VAL ASP SER SER LYS ARG GLU SER MET LYS THR GLU LEU SEQRES 7 A 383 CYS LYS GLU LEU GLN ALA LEU PRO ALA GLN ASP LEU THR SEQRES 8 A 383 LEU PHE GLU ASN GLU ILE ARG ASP GLU ASN ASN ARG ALA SEQRES 9 A 383 LEU VAL SER GLY CYS LYS GLU GLU LEU LEU ALA GLN VAL SEQRES 10 A 383 ASP GLU HIS PHE ASP GLU GLN ARG GLU SER MET SER VAL SEQRES 11 A 383 PRO GLY HIS ALA LEU LYS ALA VAL GLN SER ARG ASN SER SEQRES 12 A 383 PHE ARG PHE PRO ASP ASN THR GLN LYS ARG ASP MET SER SEQRES 13 A 383 ASN GLY TYR MET ALA VAL ARG GLY ASP VAL ALA ARG LYS SEQRES 14 A 383 GLU VAL VAL LEU THR PHE ASP ASP GLY PRO HIS GLY LEU SEQRES 15 A 383 TYR THR ASP ALA ILE LEU ARG ALA LEU LYS GLU VAL ASN SEQRES 16 A 383 ALA LYS ALA MET PHE PHE ALA THR GLY LYS SER VAL ARG SEQRES 17 A 383 THR ASN PRO GLU ALA LEU LYS ARG VAL ALA ALA ASP GLY SEQRES 18 A 383 HIS VAL ILE GLY SER HIS SER ILE THR HIS ALA CYS LEU SEQRES 19 A 383 GLY THR SER VAL ALA CYS TYR LYS GLN MET GLY ASN ARG SEQRES 20 A 383 ASN LEU THR PHE ASP GLU ALA ALA ALA GLU VAL ARG GLY SEQRES 21 A 383 GLY HIS GLN ALA VAL PHE ASP VAL LEU GLY TRP VAL ASP SEQRES 22 A 383 PRO VAL PHE ARG PHE PXU TYR GLY GLU THR SER LYS ASP SEQRES 23 A 383 LEU LYS ALA PHE LEU LYS THR LYS SER THR GLY GLU PHE SEQRES 24 A 383 ALA TRP ASN ILE GLU SER ASP ASP TRP ARG THR GLN SER SEQRES 25 A 383 ASN GLU GLN LEU LEU ALA ARG VAL LEU ALA ASN VAL GLU SEQRES 26 A 383 SER GLN GLY ARG GLY ILE VAL LEU PHE HIS ASP ILE GLN SEQRES 27 A 383 ARG ARG THR ALA GLU ILE MET PRO GLN PHE LEU ARG GLU SEQRES 28 A 383 LEU TYR ASN ARG GLY TYR SER VAL VAL LEU LEU THR ALA SEQRES 29 A 383 ALA ASP PRO SER ALA LYS TYR ASN SER LYS LEU VAL LYS SEQRES 30 A 383 ARG LYS GLN GLN LEU PRO MODRES 5JP6 PXU A 279 PRO MODIFIED RESIDUE HET PXU A 279 8 HET ZN A 401 1 HET MG A 402 1 HETNAM PXU 2-HYDROXY-L-PROLINE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 1 PXU C5 H9 N O3 FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 HOH *265(H2 O) HELIX 1 AA1 MET A 23 ALA A 40 1 18 HELIX 2 AA2 THR A 42 ASN A 48 1 7 HELIX 3 AA3 ASN A 52 ASP A 67 1 16 HELIX 4 AA4 LYS A 70 ALA A 84 1 15 HELIX 5 AA5 PRO A 86 THR A 91 1 6 HELIX 6 AA6 PHE A 93 ASP A 99 1 7 HELIX 7 AA7 ASN A 102 SER A 107 1 6 HELIX 8 AA8 CYS A 109 SER A 127 1 19 HELIX 9 AA9 LEU A 182 VAL A 194 1 13 HELIX 10 AB1 THR A 203 ASN A 210 1 8 HELIX 11 AB2 ASN A 210 ASP A 220 1 11 HELIX 12 AB3 THR A 250 GLY A 270 1 21 HELIX 13 AB4 SER A 284 LYS A 294 1 11 HELIX 14 AB5 SER A 312 GLY A 328 1 17 HELIX 15 AB6 GLN A 338 ARG A 355 1 18 HELIX 16 AB7 SER A 368 ASN A 372 5 5 SHEET 1 AA1 2 THR A 150 ARG A 153 0 SHEET 2 AA1 2 LEU A 361 ALA A 364 1 O LEU A 361 N GLN A 151 SHEET 1 AA2 8 MET A 160 ALA A 161 0 SHEET 2 AA2 8 GLY A 297 PHE A 299 1 O GLU A 298 N ALA A 161 SHEET 3 AA2 8 VAL A 275 ARG A 277 1 N PHE A 276 O PHE A 299 SHEET 4 AA2 8 VAL A 223 HIS A 227 1 N SER A 226 O ARG A 277 SHEET 5 AA2 8 MET A 199 ALA A 202 1 N PHE A 200 O VAL A 223 SHEET 6 AA2 8 GLU A 170 ASP A 176 1 N PHE A 175 O PHE A 201 SHEET 7 AA2 8 GLY A 330 HIS A 335 1 O VAL A 332 N VAL A 172 SHEET 8 AA2 8 ILE A 303 GLU A 304 1 N ILE A 303 O ILE A 331 SHEET 1 AA3 7 MET A 160 ALA A 161 0 SHEET 2 AA3 7 GLY A 297 PHE A 299 1 O GLU A 298 N ALA A 161 SHEET 3 AA3 7 VAL A 275 ARG A 277 1 N PHE A 276 O PHE A 299 SHEET 4 AA3 7 VAL A 223 HIS A 227 1 N SER A 226 O ARG A 277 SHEET 5 AA3 7 MET A 199 ALA A 202 1 N PHE A 200 O VAL A 223 SHEET 6 AA3 7 GLU A 170 ASP A 176 1 N PHE A 175 O PHE A 201 SHEET 7 AA3 7 SER A 358 VAL A 359 1 O SER A 358 N VAL A 171 SSBOND 1 CYS A 79 CYS A 109 1555 1555 2.02 LINK C PHE A 278 N PXU A 279 1555 1555 1.31 LINK C PXU A 279 N TYR A 280 1555 1555 1.32 LINK OD2 ASP A 177 ZN ZN A 401 1555 1555 2.41 LINK NE2 HIS A 227 ZN ZN A 401 1555 1555 2.06 LINK OH TYR A 280 ZN ZN A 401 1555 1555 2.30 LINK MG MG A 402 O HOH A 682 1555 1555 2.96 LINK MG MG A 402 O HOH A 734 1555 1555 2.94 CISPEP 1 GLY A 178 PRO A 179 0 4.35 SITE 1 AC1 3 ASP A 177 HIS A 227 TYR A 280 SITE 1 AC2 5 MET A 155 ALA A 365 ASP A 366 HOH A 682 SITE 2 AC2 5 HOH A 734 CRYST1 112.434 112.434 79.859 90.00 90.00 120.00 P 61 6 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 0.008894 0.005135 0.000000 0.00000 SCALE2 0.000000 0.010270 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012522 0.00000