HEADER HYDROLASE 18-JUN-09 2WKX TITLE CRYSTAL STRUCTURE OF THE NATIVE E. COLI ZINC AMIDASE AMID COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 18-276; COMPND 5 EC: 3.5.1.28; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12 MG1655; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: LMG194; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBAD/MYC-HISA KEYWDS OUTER MEMBRANE, CELL WALL BIOGENESIS/DEGRADATION, CELL MEMBRANE, KEYWDS 2 METAL-BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.PETRELLA,F.KERFF,R.HERMAN,C.GENEREUX,A.PENNARTZ,E.SAUVAGE,B.JORIS, AUTHOR 2 P.CHARLIER REVDAT 4 13-DEC-23 2WKX 1 REMARK LINK REVDAT 3 13-JUL-11 2WKX 1 VERSN REVDAT 2 09-MAR-10 2WKX 1 JRNL REVDAT 1 12-JAN-10 2WKX 0 SPRSDE 12-JAN-10 2WKX 2BGX JRNL AUTH F.KERFF,S.PETRELLA,F.MERCIER,E.SAUVAGE,R.HERMAN,A.PENNARTZ, JRNL AUTH 2 A.ZERVOSEN,A.LUXEN,J.M.FRERE,B.JORIS,P.CHARLIER JRNL TITL SPECIFIC STRUCTURAL FEATURES OF THE JRNL TITL 2 N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID FROM ESCHERICHIA JRNL TITL 3 COLI AND MECHANISTIC IMPLICATIONS FOR ENZYMES OF THIS JRNL TITL 4 FAMILY. JRNL REF J.MOL.BIOL. V. 397 249 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20036252 JRNL DOI 10.1016/J.JMB.2009.12.038 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 36115 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4027 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2022 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 219 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2056 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 19.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -0.81000 REMARK 3 B12 (A**2) : 0.27000 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): 0.089 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.842 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2168 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2958 ; 1.403 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 268 ; 5.659 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;35.761 ;23.889 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 346 ;12.471 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;11.795 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 312 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1700 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 997 ; 0.180 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1468 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 139 ; 0.127 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.113 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 73 ; 0.175 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.103 ; 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): 1362 ; 1.797 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2116 ; 2.380 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 946 ; 2.186 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 836 ; 3.383 ; 3.000 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 : 9 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 5 A 13 REMARK 3 ORIGIN FOR THE GROUP (A): 40.8667 14.7321 64.3252 REMARK 3 T TENSOR REMARK 3 T11: -0.0851 T22: 0.1608 REMARK 3 T33: 0.0616 T12: 0.1965 REMARK 3 T13: -0.1041 T23: -0.1282 REMARK 3 L TENSOR REMARK 3 L11: 18.4485 L22: 16.6279 REMARK 3 L33: 4.0129 L12: 1.5596 REMARK 3 L13: -1.0405 L23: -3.3548 REMARK 3 S TENSOR REMARK 3 S11: -0.1057 S12: 0.1892 S13: -0.0972 REMARK 3 S21: -0.1977 S22: -0.0611 S23: -1.3213 REMARK 3 S31: 0.9074 S32: 0.7572 S33: 0.1668 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 14 A 66 REMARK 3 ORIGIN FOR THE GROUP (A): 36.7731 36.5793 85.3468 REMARK 3 T TENSOR REMARK 3 T11: 0.0407 T22: 0.0720 REMARK 3 T33: 0.0453 T12: 0.0394 REMARK 3 T13: -0.0442 T23: -0.0443 REMARK 3 L TENSOR REMARK 3 L11: 0.4664 L22: 0.8433 REMARK 3 L33: 2.0721 L12: 0.4178 REMARK 3 L13: 0.7495 L23: 1.3093 REMARK 3 S TENSOR REMARK 3 S11: -0.0229 S12: 0.0702 S13: -0.1030 REMARK 3 S21: 0.1250 S22: 0.1498 S23: -0.1789 REMARK 3 S31: 0.1153 S32: 0.2611 S33: -0.1269 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 67 A 108 REMARK 3 ORIGIN FOR THE GROUP (A): 34.1465 40.2997 87.3700 REMARK 3 T TENSOR REMARK 3 T11: 0.0418 T22: 0.0435 REMARK 3 T33: 0.0177 T12: 0.0236 REMARK 3 T13: -0.0371 T23: -0.0325 REMARK 3 L TENSOR REMARK 3 L11: 1.3281 L22: 1.0840 REMARK 3 L33: 1.4360 L12: -0.0473 REMARK 3 L13: 0.8055 L23: 0.1912 REMARK 3 S TENSOR REMARK 3 S11: -0.0247 S12: 0.0754 S13: -0.0786 REMARK 3 S21: 0.0568 S22: 0.1002 S23: -0.0273 REMARK 3 S31: 0.1550 S32: 0.1527 S33: -0.0755 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 109 A 118 REMARK 3 ORIGIN FOR THE GROUP (A): 27.5411 58.3995 104.3375 REMARK 3 T TENSOR REMARK 3 T11: 0.3473 T22: 0.1357 REMARK 3 T33: 0.0248 T12: 0.4030 REMARK 3 T13: 0.0471 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 10.6652 L22: 17.6200 REMARK 3 L33: 27.0776 L12: 0.5112 REMARK 3 L13: -7.8085 L23: -1.2994 REMARK 3 S TENSOR REMARK 3 S11: -0.6067 S12: -0.5125 S13: 0.3036 REMARK 3 S21: 1.9456 S22: 1.1777 S23: 1.1687 REMARK 3 S31: -2.0703 S32: -1.5479 S33: -0.5711 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 119 A 170 REMARK 3 ORIGIN FOR THE GROUP (A): 36.4347 50.3230 86.5016 REMARK 3 T TENSOR REMARK 3 T11: 0.0269 T22: 0.0373 REMARK 3 T33: 0.0131 T12: -0.0010 REMARK 3 T13: -0.0495 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 1.4403 L22: 1.0711 REMARK 3 L33: 1.5301 L12: -0.4472 REMARK 3 L13: 0.2120 L23: 0.2868 REMARK 3 S TENSOR REMARK 3 S11: -0.1078 S12: 0.0699 S13: 0.0360 REMARK 3 S21: 0.0224 S22: 0.0963 S23: -0.0818 REMARK 3 S31: -0.1064 S32: 0.1657 S33: 0.0115 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 171 A 214 REMARK 3 ORIGIN FOR THE GROUP (A): 27.6981 64.1424 78.2674 REMARK 3 T TENSOR REMARK 3 T11: 0.1000 T22: 0.0030 REMARK 3 T33: 0.0094 T12: -0.0246 REMARK 3 T13: -0.0739 T23: 0.0213 REMARK 3 L TENSOR REMARK 3 L11: 1.1121 L22: 1.3168 REMARK 3 L33: 1.1200 L12: -0.4086 REMARK 3 L13: 0.2111 L23: -0.1285 REMARK 3 S TENSOR REMARK 3 S11: -0.0765 S12: 0.0299 S13: 0.1170 REMARK 3 S21: -0.0551 S22: 0.0404 S23: -0.0303 REMARK 3 S31: -0.2760 S32: 0.0778 S33: 0.0362 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 215 A 221 REMARK 3 ORIGIN FOR THE GROUP (A): 10.5742 55.7444 85.7095 REMARK 3 T TENSOR REMARK 3 T11: -0.0840 T22: 0.0516 REMARK 3 T33: 0.1021 T12: 0.0667 REMARK 3 T13: -0.0234 T23: 0.0512 REMARK 3 L TENSOR REMARK 3 L11: 12.5528 L22: 18.7836 REMARK 3 L33: 40.9905 L12: 3.1563 REMARK 3 L13: 4.9315 L23: 18.0359 REMARK 3 S TENSOR REMARK 3 S11: 0.0705 S12: 0.0485 S13: -0.8357 REMARK 3 S21: 0.2894 S22: -0.0785 S23: 0.6116 REMARK 3 S31: 0.5832 S32: -0.8935 S33: 0.0080 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 222 A 231 REMARK 3 ORIGIN FOR THE GROUP (A): 20.0040 59.0825 87.7619 REMARK 3 T TENSOR REMARK 3 T11: 0.0840 T22: 0.0116 REMARK 3 T33: 0.0190 T12: 0.0516 REMARK 3 T13: -0.0544 T23: -0.0132 REMARK 3 L TENSOR REMARK 3 L11: 14.8349 L22: 6.2511 REMARK 3 L33: 3.2848 L12: 4.5913 REMARK 3 L13: 1.2175 L23: -3.4140 REMARK 3 S TENSOR REMARK 3 S11: -0.0532 S12: -0.3010 S13: 0.4016 REMARK 3 S21: 0.1412 S22: 0.1330 S23: 0.3359 REMARK 3 S31: -0.2559 S32: -0.2117 S33: -0.0798 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 232 A 261 REMARK 3 ORIGIN FOR THE GROUP (A): 27.5632 63.3946 81.3959 REMARK 3 T TENSOR REMARK 3 T11: 0.0962 T22: -0.0105 REMARK 3 T33: 0.0306 T12: -0.0046 REMARK 3 T13: -0.0853 T23: 0.0205 REMARK 3 L TENSOR REMARK 3 L11: 1.2155 L22: 1.1614 REMARK 3 L33: 2.4669 L12: -0.6501 REMARK 3 L13: 0.1622 L23: 0.3247 REMARK 3 S TENSOR REMARK 3 S11: -0.0960 S12: 0.0488 S13: 0.1594 REMARK 3 S21: 0.0320 S22: 0.0189 S23: -0.0310 REMARK 3 S31: -0.3653 S32: 0.0620 S33: 0.0770 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2WKX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1290040164. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41725 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 21.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 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 2BH7 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M LICL, 10 % PEG 6K, 0.1M ZNCL2, PH 4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 61.30767 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 122.61533 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 91.96150 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 153.26917 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 30.65383 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.30767 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 122.61533 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 153.26917 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 91.96150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 30.65383 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -123.0 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 0.500000 -0.866025 0.000000 44.49500 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 77.06760 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 153.26917 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 GLY A 2 REMARK 465 ALA A 3 REMARK 465 GLY A 4 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 ASP A 50 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 140 NE - CZ - NH2 ANGL. DEV. = 4.1 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 ARG A 235 56.98 -145.98 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 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 35 ND1 REMARK 620 2 HIS A 151 ND1 93.0 REMARK 620 3 ASP A 161 OD1 104.9 124.0 REMARK 620 4 CL A 302 CL 120.4 99.8 114.2 REMARK 620 N 1 2 3 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BGX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NATIVE AMID AT 1.8 ANGSTROM REMARK 900 RELATED ID: 2BH7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A SEMET DERIVATIVE OF AMID AT 2.2 ANGSTROMS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE N-TERMINAL CYSTEINE OF THE PROCESSED PROTEIN WAS REMARK 999 REPLACED BY A GLYCINE. A METHIONINE WAS ADDED AT THE N- REMARK 999 TERMINUS. DBREF 2WKX A 1 2 PDB 2WKX 2WKX 1 2 DBREF 2WKX A 3 261 UNP P75820 AMID_ECOLI 18 276 SEQRES 1 A 261 MET GLY ALA GLY GLU LYS GLY ILE VAL GLU LYS GLU GLY SEQRES 2 A 261 TYR GLN LEU ASP THR ARG ARG GLN ALA GLN ALA ALA TYR SEQRES 3 A 261 PRO ARG ILE LYS VAL LEU VAL ILE HIS TYR THR ALA ASP SEQRES 4 A 261 ASP PHE ASP SER SER LEU ALA THR LEU THR ASP LYS GLN SEQRES 5 A 261 VAL SER SER HIS TYR LEU VAL PRO ALA VAL PRO PRO ARG SEQRES 6 A 261 TYR ASN GLY LYS PRO ARG ILE TRP GLN LEU VAL PRO GLU SEQRES 7 A 261 GLN GLU LEU ALA TRP HIS ALA GLY ILE SER ALA TRP ARG SEQRES 8 A 261 GLY ALA THR ARG LEU ASN ASP THR SER ILE GLY ILE GLU SEQRES 9 A 261 LEU GLU ASN ARG GLY TRP GLN LYS SER ALA GLY VAL LYS SEQRES 10 A 261 TYR PHE ALA PRO PHE GLU PRO ALA GLN ILE GLN ALA LEU SEQRES 11 A 261 ILE PRO LEU ALA LYS ASP ILE ILE ALA ARG TYR HIS ILE SEQRES 12 A 261 LYS PRO GLU ASN VAL VAL ALA HIS ALA ASP ILE ALA PRO SEQRES 13 A 261 GLN ARG LYS ASP ASP PRO GLY PRO LEU PHE PRO TRP GLN SEQRES 14 A 261 GLN LEU ALA GLN GLN GLY ILE GLY ALA TRP PRO ASP ALA SEQRES 15 A 261 GLN ARG VAL ASN PHE TYR LEU ALA GLY ARG ALA PRO HIS SEQRES 16 A 261 THR PRO VAL ASP THR ALA SER LEU LEU GLU LEU LEU ALA SEQRES 17 A 261 ARG TYR GLY TYR ASP VAL LYS PRO ASP MET THR PRO ARG SEQRES 18 A 261 GLU GLN ARG ARG VAL ILE MET ALA PHE GLN MET HIS PHE SEQRES 19 A 261 ARG PRO THR LEU TYR ASN GLY GLU ALA ASP ALA GLU THR SEQRES 20 A 261 GLN ALA ILE ALA GLU ALA LEU LEU GLU LYS TYR GLY GLN SEQRES 21 A 261 ASP HET ZN A 300 1 HET CL A 301 1 HET CL A 302 1 HET GOL A 303 6 HET GOL A 304 6 HET GOL A 305 6 HET GOL A 306 6 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 CL 2(CL 1-) FORMUL 5 GOL 4(C3 H8 O3) FORMUL 9 HOH *239(H2 O) HELIX 1 1 ASP A 40 THR A 49 1 10 HELIX 2 2 LEU A 96 ASP A 98 5 3 HELIX 3 3 GLU A 123 HIS A 142 1 20 HELIX 4 4 LYS A 144 GLU A 146 5 3 HELIX 5 5 HIS A 151 ALA A 155 1 5 HELIX 6 6 PRO A 167 GLN A 174 1 8 HELIX 7 7 ASP A 181 ALA A 190 1 10 HELIX 8 8 ASP A 199 GLY A 211 1 13 HELIX 9 9 THR A 219 ARG A 235 1 17 HELIX 10 10 ASP A 244 GLY A 259 1 16 SHEET 1 AA 2 ILE A 8 GLU A 10 0 SHEET 2 AA 2 GLN A 15 ASP A 17 -1 O LEU A 16 N VAL A 9 SHEET 1 AB 5 TRP A 73 GLN A 74 0 SHEET 2 AB 5 TYR A 57 VAL A 59 -1 O LEU A 58 N TRP A 73 SHEET 3 AB 5 SER A 100 LEU A 105 1 O GLY A 102 N TYR A 57 SHEET 4 AB 5 VAL A 31 TYR A 36 1 O VAL A 31 N ILE A 101 SHEET 5 AB 5 VAL A 148 ALA A 150 1 O VAL A 149 N ILE A 34 SHEET 1 AC 2 ARG A 65 TYR A 66 0 SHEET 2 AC 2 LYS A 69 PRO A 70 -1 O LYS A 69 N TYR A 66 SHEET 1 AD 2 ALA A 89 TRP A 90 0 SHEET 2 AD 2 ALA A 93 THR A 94 -1 O ALA A 93 N TRP A 90 SHEET 1 AE 2 TRP A 110 SER A 113 0 SHEET 2 AE 2 VAL A 116 PHE A 119 -1 O VAL A 116 N SER A 113 LINK ND1 HIS A 35 ZN ZN A 300 1555 1555 2.14 LINK ND1 HIS A 151 ZN ZN A 300 1555 1555 2.11 LINK OD1 ASP A 161 ZN ZN A 300 1555 1555 1.95 LINK ZN ZN A 300 CL CL A 302 1555 1555 2.27 CISPEP 1 ASP A 161 PRO A 162 0 2.34 SITE 1 AC1 4 HIS A 35 HIS A 151 ASP A 161 CL A 302 SITE 1 AC2 4 ALA A 85 GLY A 86 HIS A 151 ARG A 158 SITE 1 AC3 5 HIS A 151 LYS A 159 ASP A 161 ZN A 300 SITE 2 AC3 5 HOH A2091 SITE 1 AC4 8 ALA A 201 LYS A 215 PRO A 216 ASP A 217 SITE 2 AC4 8 MET A 218 HOH A2036 HOH A2235 HOH A2236 SITE 1 AC5 9 PRO A 145 ALA A 172 GLY A 175 ILE A 176 SITE 2 AC5 9 GLY A 177 LYS A 257 TYR A 258 GOL A 305 SITE 3 AC5 9 HOH A2238 SITE 1 AC6 8 GLN A 173 TRP A 179 PRO A 180 ASP A 181 SITE 2 AC6 8 LYS A 257 GOL A 304 HOH A2238 HOH A2239 SITE 1 AC7 8 VAL A 31 TRP A 90 ARG A 91 ALA A 93 SITE 2 AC7 8 ARG A 95 ASN A 147 ASP A 261 HOH A2089 CRYST1 88.990 88.990 183.923 90.00 90.00 120.00 P 61 2 2 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 0.011237 0.006488 0.000000 0.00000 SCALE2 0.000000 0.012976 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005437 0.00000