HEADER ISOMERASE 24-DEC-12 4IK0 TITLE CRYSTAL STRUCTURE OF DIAMINOPIMELATE EPIMERASE Y268A MUTANT FROM TITLE 2 ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE EPIMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DAP EPIMERASE; COMPND 5 EC: 5.1.1.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: DAPF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS DAP EPIMERASE-LIKE, ISOMERASE, CYTOSOL EXPDTA X-RAY DIFFRACTION AUTHOR L.HOR,R.C.J.DOBSON,C.A.HUTTON,M.A.PERUGINI REVDAT 4 20-MAR-24 4IK0 1 REMARK SEQADV REVDAT 3 17-APR-13 4IK0 1 JRNL REVDAT 2 06-MAR-13 4IK0 1 JRNL REVDAT 1 20-FEB-13 4IK0 0 JRNL AUTH L.HOR,R.C.J.DOBSON,M.T.DOWNTON,J.WAGNER,C.A.HUTTON, JRNL AUTH 2 M.A.PERUGINI JRNL TITL DIMERIZATION OF BACTERIAL DIAMINOPIMELATE EPIMERASE IS JRNL TITL 2 ESSENTIAL FOR CATALYSIS JRNL REF J.BIOL.CHEM. V. 288 9238 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23426375 JRNL DOI 10.1074/JBC.M113.450148 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 46242 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1863 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2942 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4224 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 395 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.08000 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): 0.156 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.494 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4329 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5866 ; 1.652 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 551 ; 6.834 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 210 ;33.131 ;23.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 701 ;13.094 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;22.539 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 647 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3366 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 6 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 1 A 111 REMARK 3 ORIGIN FOR THE GROUP (A): 9.2657 -9.0428 -9.8987 REMARK 3 T TENSOR REMARK 3 T11: 0.0633 T22: 0.0315 REMARK 3 T33: 0.0301 T12: 0.0247 REMARK 3 T13: 0.0042 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 1.9391 L22: 1.0443 REMARK 3 L33: 1.4506 L12: -0.7279 REMARK 3 L13: 0.6482 L23: -0.6309 REMARK 3 S TENSOR REMARK 3 S11: 0.0799 S12: 0.1165 S13: -0.0453 REMARK 3 S21: -0.0670 S22: -0.0653 S23: 0.0230 REMARK 3 S31: 0.0368 S32: 0.0751 S33: -0.0147 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 112 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0948 -34.1222 -16.1675 REMARK 3 T TENSOR REMARK 3 T11: 0.0898 T22: 0.0160 REMARK 3 T33: 0.0521 T12: 0.0281 REMARK 3 T13: -0.0020 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 2.4351 L22: 2.9028 REMARK 3 L33: 1.2480 L12: -1.7018 REMARK 3 L13: -0.9426 L23: 0.8483 REMARK 3 S TENSOR REMARK 3 S11: 0.0861 S12: 0.0730 S13: 0.0341 REMARK 3 S21: -0.2208 S22: -0.1504 S23: -0.0316 REMARK 3 S31: 0.0054 S32: 0.0295 S33: 0.0643 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 263 A 273 REMARK 3 ORIGIN FOR THE GROUP (A): 5.7826 -8.4305 1.2698 REMARK 3 T TENSOR REMARK 3 T11: 0.1236 T22: 0.0680 REMARK 3 T33: 0.0128 T12: 0.0267 REMARK 3 T13: 0.0011 T23: 0.0155 REMARK 3 L TENSOR REMARK 3 L11: 2.8532 L22: 11.2346 REMARK 3 L33: 9.5325 L12: 1.4098 REMARK 3 L13: 0.0510 L23: 9.3298 REMARK 3 S TENSOR REMARK 3 S11: 0.0846 S12: -0.2094 S13: 0.0141 REMARK 3 S21: -0.5167 S22: -0.0206 S23: 0.0262 REMARK 3 S31: -0.5444 S32: 0.0644 S33: -0.0639 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 : B 1 B 111 REMARK 3 ORIGIN FOR THE GROUP (A): 9.3088 -7.6757 21.4741 REMARK 3 T TENSOR REMARK 3 T11: 0.0467 T22: 0.0553 REMARK 3 T33: 0.0305 T12: 0.0036 REMARK 3 T13: -0.0022 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 1.0840 L22: 1.4992 REMARK 3 L33: 0.9836 L12: -0.0231 REMARK 3 L13: 0.3877 L23: 0.0328 REMARK 3 S TENSOR REMARK 3 S11: 0.0307 S12: -0.0884 S13: 0.0078 REMARK 3 S21: 0.1058 S22: -0.0041 S23: -0.0731 REMARK 3 S31: -0.0013 S32: -0.0487 S33: -0.0265 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 : B 112 B 250 REMARK 3 ORIGIN FOR THE GROUP (A): 34.3950 -13.9691 27.3996 REMARK 3 T TENSOR REMARK 3 T11: 0.0512 T22: 0.0300 REMARK 3 T33: 0.0559 T12: -0.0015 REMARK 3 T13: -0.0360 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 2.9390 L22: 1.7676 REMARK 3 L33: 1.6202 L12: -1.3634 REMARK 3 L13: 0.4416 L23: -0.4777 REMARK 3 S TENSOR REMARK 3 S11: 0.0590 S12: 0.0465 S13: -0.2376 REMARK 3 S21: -0.0836 S22: -0.0125 S23: 0.0550 REMARK 3 S31: 0.1863 S32: 0.1460 S33: -0.0465 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 : B 251 B 275 REMARK 3 ORIGIN FOR THE GROUP (A): 16.7467 -4.6942 22.5165 REMARK 3 T TENSOR REMARK 3 T11: 0.0790 T22: 0.0392 REMARK 3 T33: 0.0311 T12: -0.0100 REMARK 3 T13: -0.0133 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 3.8850 L22: 0.2375 REMARK 3 L33: 5.1897 L12: -0.1443 REMARK 3 L13: 4.0446 L23: -0.0078 REMARK 3 S TENSOR REMARK 3 S11: 0.1017 S12: -0.1864 S13: 0.0029 REMARK 3 S21: 0.0294 S22: -0.0238 S23: -0.0071 REMARK 3 S31: 0.1117 S32: -0.2045 S33: -0.0779 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4IK0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000076848. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46324 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 49.677 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12600 REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.57700 REMARK 200 R SYM FOR SHELL (I) : 0.57700 REMARK 200 FOR SHELL : 1.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM IODIDE, 18% PEG 3350, 0.1M REMARK 280 BIS-TRIS PROPANE, 5MM DIAMINOPIMELIC ACID, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 89.72500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.59000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.59000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.86250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.59000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.59000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 134.58750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.59000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.59000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.86250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.59000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.59000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 134.58750 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 89.72500 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 HIS A 275 REMARK 465 HIS A 276 REMARK 465 HIS A 277 REMARK 465 HIS A 278 REMARK 465 HIS A 279 REMARK 465 HIS A 280 REMARK 465 HIS B 276 REMARK 465 HIS B 277 REMARK 465 HIS B 278 REMARK 465 HIS B 279 REMARK 465 HIS B 280 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 72 CG CD OE1 NE2 REMARK 470 GLU B 145 CG CD OE1 OE2 REMARK 470 GLU B 183 CG CD OE1 OE2 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 O HOH B 587 O HOH B 588 1.71 REMARK 500 O HOH B 610 O HOH B 611 1.89 REMARK 500 O HOH A 574 O HOH A 575 2.01 REMARK 500 OE2 GLU A 208 CG2 THR A 214 2.03 REMARK 500 O HOH B 438 O HOH B 511 2.12 REMARK 500 OE1 GLU B 28 O HOH B 613 2.13 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 HIS A 7 CG HIS A 7 CD2 0.065 REMARK 500 HIS A 159 CG HIS A 159 CD2 0.054 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 B 78 CD - NE - CZ ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG B 78 NE - CZ - NH1 ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG B 78 NE - CZ - NH2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG B 82 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 82 NE - CZ - NH2 ANGL. DEV. = -6.2 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 ALA A 144 -129.22 49.48 REMARK 500 ARG A 188 174.40 66.22 REMARK 500 ARG A 188 171.59 71.42 REMARK 500 ALA B 144 -93.26 24.53 REMARK 500 ARG B 188 178.28 66.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IJZ RELATED DB: PDB DBREF 4IK0 A 1 274 UNP P0A6K1 DAPF_ECOLI 1 274 DBREF 4IK0 B 1 274 UNP P0A6K1 DAPF_ECOLI 1 274 SEQADV 4IK0 ALA A 268 UNP P0A6K1 TYR 268 ENGINEERED MUTATION SEQADV 4IK0 HIS A 275 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 HIS A 276 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 HIS A 277 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 HIS A 278 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 HIS A 279 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 HIS A 280 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 ALA B 268 UNP P0A6K1 TYR 268 ENGINEERED MUTATION SEQADV 4IK0 HIS B 275 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 HIS B 276 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 HIS B 277 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 HIS B 278 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 HIS B 279 UNP P0A6K1 EXPRESSION TAG SEQADV 4IK0 HIS B 280 UNP P0A6K1 EXPRESSION TAG SEQRES 1 A 280 MET GLN PHE SER LYS MET HIS GLY LEU GLY ASN ASP PHE SEQRES 2 A 280 MET VAL VAL ASP ALA VAL THR GLN ASN VAL PHE PHE SER SEQRES 3 A 280 PRO GLU LEU ILE ARG ARG LEU ALA ASP ARG HIS LEU GLY SEQRES 4 A 280 VAL GLY PHE ASP GLN LEU LEU VAL VAL GLU PRO PRO TYR SEQRES 5 A 280 ASP PRO GLU LEU ASP PHE HIS TYR ARG ILE PHE ASN ALA SEQRES 6 A 280 ASP GLY SER GLU VAL ALA GLN CYS GLY ASN GLY ALA ARG SEQRES 7 A 280 CYS PHE ALA ARG PHE VAL ARG LEU LYS GLY LEU THR ASN SEQRES 8 A 280 LYS ARG ASP ILE ARG VAL SER THR ALA ASN GLY ARG MET SEQRES 9 A 280 VAL LEU THR VAL THR ASP ASP ASP LEU VAL ARG VAL ASN SEQRES 10 A 280 MET GLY GLU PRO ASN PHE GLU PRO SER ALA VAL PRO PHE SEQRES 11 A 280 ARG ALA ASN LYS ALA GLU LYS THR TYR ILE MET ARG ALA SEQRES 12 A 280 ALA GLU GLN THR ILE LEU CYS GLY VAL VAL SER MET GLY SEQRES 13 A 280 ASN PRO HIS CYS VAL ILE GLN VAL ASP ASP VAL ASP THR SEQRES 14 A 280 ALA ALA VAL GLU THR LEU GLY PRO VAL LEU GLU SER HIS SEQRES 15 A 280 GLU ARG PHE PRO GLU ARG ALA ASN ILE GLY PHE MET GLN SEQRES 16 A 280 VAL VAL LYS ARG GLU HIS ILE ARG LEU ARG VAL TYR GLU SEQRES 17 A 280 ARG GLY ALA GLY GLU THR GLN ALA CYS GLY SER GLY ALA SEQRES 18 A 280 CYS ALA ALA VAL ALA VAL GLY ILE GLN GLN GLY LEU LEU SEQRES 19 A 280 ALA GLU GLU VAL ARG VAL GLU LEU PRO GLY GLY ARG LEU SEQRES 20 A 280 ASP ILE ALA TRP LYS GLY PRO GLY HIS PRO LEU TYR MET SEQRES 21 A 280 THR GLY PRO ALA VAL HIS VAL ALA ASP GLY PHE ILE HIS SEQRES 22 A 280 LEU HIS HIS HIS HIS HIS HIS SEQRES 1 B 280 MET GLN PHE SER LYS MET HIS GLY LEU GLY ASN ASP PHE SEQRES 2 B 280 MET VAL VAL ASP ALA VAL THR GLN ASN VAL PHE PHE SER SEQRES 3 B 280 PRO GLU LEU ILE ARG ARG LEU ALA ASP ARG HIS LEU GLY SEQRES 4 B 280 VAL GLY PHE ASP GLN LEU LEU VAL VAL GLU PRO PRO TYR SEQRES 5 B 280 ASP PRO GLU LEU ASP PHE HIS TYR ARG ILE PHE ASN ALA SEQRES 6 B 280 ASP GLY SER GLU VAL ALA GLN CYS GLY ASN GLY ALA ARG SEQRES 7 B 280 CYS PHE ALA ARG PHE VAL ARG LEU LYS GLY LEU THR ASN SEQRES 8 B 280 LYS ARG ASP ILE ARG VAL SER THR ALA ASN GLY ARG MET SEQRES 9 B 280 VAL LEU THR VAL THR ASP ASP ASP LEU VAL ARG VAL ASN SEQRES 10 B 280 MET GLY GLU PRO ASN PHE GLU PRO SER ALA VAL PRO PHE SEQRES 11 B 280 ARG ALA ASN LYS ALA GLU LYS THR TYR ILE MET ARG ALA SEQRES 12 B 280 ALA GLU GLN THR ILE LEU CYS GLY VAL VAL SER MET GLY SEQRES 13 B 280 ASN PRO HIS CYS VAL ILE GLN VAL ASP ASP VAL ASP THR SEQRES 14 B 280 ALA ALA VAL GLU THR LEU GLY PRO VAL LEU GLU SER HIS SEQRES 15 B 280 GLU ARG PHE PRO GLU ARG ALA ASN ILE GLY PHE MET GLN SEQRES 16 B 280 VAL VAL LYS ARG GLU HIS ILE ARG LEU ARG VAL TYR GLU SEQRES 17 B 280 ARG GLY ALA GLY GLU THR GLN ALA CYS GLY SER GLY ALA SEQRES 18 B 280 CYS ALA ALA VAL ALA VAL GLY ILE GLN GLN GLY LEU LEU SEQRES 19 B 280 ALA GLU GLU VAL ARG VAL GLU LEU PRO GLY GLY ARG LEU SEQRES 20 B 280 ASP ILE ALA TRP LYS GLY PRO GLY HIS PRO LEU TYR MET SEQRES 21 B 280 THR GLY PRO ALA VAL HIS VAL ALA ASP GLY PHE ILE HIS SEQRES 22 B 280 LEU HIS HIS HIS HIS HIS HIS HET IOD A 301 1 HET IOD A 302 1 HET IOD A 303 1 HET IOD A 304 1 HET IOD A 305 1 HET IOD A 306 1 HET IOD B 301 1 HET IOD B 302 1 HET IOD B 303 1 HET IOD B 304 1 HET IOD B 305 1 HET IOD B 306 1 HET IOD B 307 1 HETNAM IOD IODIDE ION FORMUL 3 IOD 13(I 1-) FORMUL 16 HOH *395(H2 O) HELIX 1 1 SER A 26 ASP A 35 1 10 HELIX 2 2 GLY A 76 LYS A 87 1 12 HELIX 3 3 GLU A 124 VAL A 128 5 5 HELIX 4 4 ALA A 171 SER A 181 1 11 HELIX 5 5 CYS A 217 GLN A 231 1 15 HELIX 6 6 SER B 26 ASP B 35 1 10 HELIX 7 7 GLY B 76 LYS B 87 1 12 HELIX 8 8 GLU B 124 VAL B 128 5 5 HELIX 9 9 ASP B 166 ALA B 170 5 5 HELIX 10 10 ALA B 171 SER B 181 1 11 HELIX 11 11 CYS B 217 GLN B 231 1 15 SHEET 1 A 6 TYR B 139 ALA B 143 0 SHEET 2 A 6 GLN B 146 SER B 154 -1 O CYS B 150 N TYR B 139 SHEET 3 A 6 PRO B 158 GLN B 163 -1 O VAL B 161 N GLY B 151 SHEET 4 A 6 ASN B 190 LYS B 198 1 O MET B 194 N ILE B 162 SHEET 5 A 6 HIS B 201 GLU B 208 -1 O TYR B 207 N ILE B 191 SHEET 6 A 6 GLY B 212 GLU B 213 -1 O GLY B 212 N GLU B 208 SHEET 1 B10 GLY B 212 GLU B 213 0 SHEET 2 B10 HIS B 201 GLU B 208 -1 N GLU B 208 O GLY B 212 SHEET 3 B10 GLU B 237 LEU B 242 1 O ARG B 239 N ILE B 202 SHEET 4 B10 GLY B 245 TRP B 251 -1 O LEU B 247 N VAL B 240 SHEET 5 B10 LEU B 258 GLY B 262 -1 O TYR B 259 N ALA B 250 SHEET 6 B10 VAL B 114 ASN B 117 -1 N VAL B 116 O MET B 260 SHEET 7 B10 GLY B 102 VAL B 108 -1 N THR B 107 O ARG B 115 SHEET 8 B10 ASP B 94 THR B 99 -1 N VAL B 97 O MET B 104 SHEET 9 B10 PHE B 58 ASN B 64 1 N TYR B 60 O SER B 98 SHEET 10 B10 GLU B 69 VAL B 70 -1 O VAL B 70 N ILE B 62 SHEET 1 C12 GLU B 69 VAL B 70 0 SHEET 2 C12 PHE B 58 ASN B 64 -1 N ILE B 62 O VAL B 70 SHEET 3 C12 GLN B 44 GLU B 49 -1 N GLU B 49 O HIS B 59 SHEET 4 C12 ASN B 11 ASP B 17 1 N MET B 14 O LEU B 46 SHEET 5 C12 GLN B 2 GLY B 8 -1 N SER B 4 O VAL B 15 SHEET 6 C12 VAL B 265 PHE B 271 -1 O VAL B 265 N HIS B 7 SHEET 7 C12 VAL A 265 ILE A 272 -1 N PHE A 271 O ASP B 269 SHEET 8 C12 GLN A 2 GLY A 8 -1 N HIS A 7 O VAL A 265 SHEET 9 C12 ASN A 11 ASP A 17 -1 O PHE A 13 N MET A 6 SHEET 10 C12 GLN A 44 GLU A 49 1 O VAL A 48 N VAL A 16 SHEET 11 C12 PHE A 58 ASN A 64 -1 O HIS A 59 N GLU A 49 SHEET 12 C12 GLU A 69 VAL A 70 -1 O VAL A 70 N ILE A 62 SHEET 1 D13 GLU A 69 VAL A 70 0 SHEET 2 D13 PHE A 58 ASN A 64 -1 N ILE A 62 O VAL A 70 SHEET 3 D13 ASP A 94 THR A 99 1 O SER A 98 N TYR A 60 SHEET 4 D13 GLY A 102 VAL A 108 -1 O LEU A 106 N ILE A 95 SHEET 5 D13 VAL A 114 ASN A 117 -1 O ARG A 115 N THR A 107 SHEET 6 D13 LEU A 258 GLY A 262 -1 O MET A 260 N VAL A 116 SHEET 7 D13 GLY A 245 TRP A 251 -1 N ASP A 248 O THR A 261 SHEET 8 D13 GLU A 237 LEU A 242 -1 N VAL A 240 O LEU A 247 SHEET 9 D13 HIS A 201 GLU A 208 1 N ILE A 202 O ARG A 239 SHEET 10 D13 ASN A 190 LYS A 198 -1 N PHE A 193 O ARG A 205 SHEET 11 D13 PRO A 158 VAL A 164 1 N ILE A 162 O MET A 194 SHEET 12 D13 GLN A 146 SER A 154 -1 N GLY A 151 O VAL A 161 SHEET 13 D13 TYR A 139 ALA A 143 -1 N TYR A 139 O CYS A 150 SHEET 1 E 6 GLY A 212 THR A 214 0 SHEET 2 E 6 HIS A 201 GLU A 208 -1 N GLU A 208 O GLY A 212 SHEET 3 E 6 ASN A 190 LYS A 198 -1 N PHE A 193 O ARG A 205 SHEET 4 E 6 PRO A 158 VAL A 164 1 N ILE A 162 O MET A 194 SHEET 5 E 6 GLN A 146 SER A 154 -1 N GLY A 151 O VAL A 161 SHEET 6 E 6 TYR A 139 ALA A 143 -1 N TYR A 139 O CYS A 150 CISPEP 1 VAL A 128 PRO A 129 0 -9.25 CISPEP 2 VAL B 128 PRO B 129 0 -6.84 SITE 1 AC1 1 CYS A 79 SITE 1 AC2 1 ARG A 78 SITE 1 AC3 2 ALA A 171 LEU A 175 SITE 1 AC4 1 HIS A 201 SITE 1 AC5 1 ASN B 133 SITE 1 AC6 2 ASN B 11 ARG B 78 SITE 1 AC7 1 ALA B 171 SITE 1 AC8 1 VAL B 105 SITE 1 AC9 1 HIS B 201 SITE 1 BC1 1 HIS B 37 CRYST1 89.180 89.180 179.450 90.00 90.00 90.00 P 41 21 2 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 0.011213 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011213 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005573 0.00000