HEADER HYDROLASE 16-JAN-15 4XP8 TITLE STRUCTURE OF ETGA D60N MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ETGA PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 19-104; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ETGA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PEPTIDOGLYCAN HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.J.BURKINSHAW,L.J.WORRALL,N.C.J.STRYNADKA REVDAT 6 08-JAN-20 4XP8 1 REMARK REVDAT 5 22-NOV-17 4XP8 1 REMARK REVDAT 4 06-SEP-17 4XP8 1 SOURCE JRNL REMARK REVDAT 3 29-APR-15 4XP8 1 JRNL REVDAT 2 04-MAR-15 4XP8 1 JRNL REVDAT 1 18-FEB-15 4XP8 0 JRNL AUTH B.J.BURKINSHAW,W.DENG,E.LAMEIGNERE,G.A.WASNEY,H.ZHU, JRNL AUTH 2 L.J.WORRALL,B.B.FINLAY,N.C.STRYNADKA JRNL TITL STRUCTURAL ANALYSIS OF A SPECIALIZED TYPE III SECRETION JRNL TITL 2 SYSTEM PEPTIDOGLYCAN-CLEAVING ENZYME. JRNL REF J.BIOL.CHEM. V. 290 10406 2015 JRNL REFN ESSN 1083-351X JRNL PMID 25678709 JRNL DOI 10.1074/JBC.M115.639013 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 6064 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 607 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) : 2.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 404 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 685 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.63000 REMARK 3 B22 (A**2) : 0.63000 REMARK 3 B33 (A**2) : -2.04000 REMARK 3 B12 (A**2) : 0.31000 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): 0.219 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.181 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.174 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 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): 700 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 688 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 946 ; 1.454 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1585 ; 0.946 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 90 ;12.021 ; 5.278 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 29 ;42.850 ;27.241 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 128 ;14.608 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 109 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 807 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 151 ; 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): 353 ; 2.294 ; 2.530 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 352 ; 2.270 ; 2.523 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 440 ; 3.182 ; 3.778 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): 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 19 A 105 REMARK 3 ORIGIN FOR THE GROUP (A): 25.0450 24.0620 -9.5540 REMARK 3 T TENSOR REMARK 3 T11: 0.0346 T22: 0.0699 REMARK 3 T33: 0.0043 T12: -0.0093 REMARK 3 T13: -0.0059 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 2.3654 L22: 3.3942 REMARK 3 L33: 5.6428 L12: -0.5840 REMARK 3 L13: 0.2371 L23: -0.4856 REMARK 3 S TENSOR REMARK 3 S11: 0.0821 S12: 0.2450 S13: -0.0724 REMARK 3 S21: -0.2077 S22: -0.0296 S23: 0.0465 REMARK 3 S31: 0.2403 S32: -0.0931 S33: -0.0525 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 4XP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795, 0.9797, 0.9611 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.14, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6064 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 29.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.75800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: DIAMOND-SHAPED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE, PH 7.3, 20% 2 REMARK 280 -PROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 49.84333 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 99.68667 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 99.68667 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 49.84333 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 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 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 ASN A 102 35.13 -99.26 REMARK 500 REMARK 500 REMARK: NULL DBREF 4XP8 A 19 104 UNP C7BUG6 C7BUG6_ECOLX 19 104 SEQADV 4XP8 MSE A 18 UNP C7BUG6 INITIATING METHIONINE SEQADV 4XP8 ASN A 60 UNP C7BUG6 ASP 60 ENGINEERED MUTATION SEQADV 4XP8 TYR A 105 UNP C7BUG6 EXPRESSION TAG SEQRES 1 A 88 MSE ASP CYS PHE GLU ILE THR GLY LYS ALA TYR ASN ILE SEQRES 2 A 88 ASP PRO LEU ILE LEU LYS ALA ILE ALA TRP ASN GLU SER SEQRES 3 A 88 LYS ASN LYS ASN GLY ILE LYS SER LYS ILE ASN LYS ASN SEQRES 4 A 88 GLY THR TYR ASN ILE GLY ILE MSE GLN ILE ASN SER SER SEQRES 5 A 88 HIS LEU ASP LEU LEU SER LYS PHE ASN ILE SER GLU ASP SEQRES 6 A 88 ASP LEU LEU ASN ASP ALA CYS ILE ASN ILE SER VAL ALA SEQRES 7 A 88 GLY TYR ILE LEU ALA SER ASN ILE LYS TYR MODRES 4XP8 MSE A 64 MET MODIFIED RESIDUE HET MSE A 18 8 HET MSE A 64 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *17(H2 O) HELIX 1 AA1 ASP A 19 ASN A 29 1 11 HELIX 2 AA2 ASP A 31 LYS A 44 1 14 HELIX 3 AA3 HIS A 70 PHE A 77 1 8 HELIX 4 AA4 SER A 80 ASP A 87 1 8 HELIX 5 AA5 ASP A 87 SER A 101 1 15 SHEET 1 AA1 2 ASN A 60 ILE A 61 0 SHEET 2 AA1 2 ILE A 66 ASN A 67 -1 O ILE A 66 N ILE A 61 SSBOND 1 CYS A 20 CYS A 89 1555 1555 2.04 LINK C MSE A 18 N ASP A 19 1555 1555 1.33 LINK C ILE A 63 N MSE A 64 1555 1555 1.33 LINK C MSE A 64 N GLN A 65 1555 1555 1.33 CRYST1 31.400 31.400 149.530 90.00 90.00 120.00 P 31 2 1 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 0.031847 0.018387 0.000000 0.00000 SCALE2 0.000000 0.036774 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006688 0.00000 MASTER 280 0 2 5 2 0 0 6 0 0 0 7 END