HEADER HYDROLASE 04-FEB-05 1YRR TITLE CRYSTAL STRUCTURE OF THE N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE TITLE 2 FROM ESCHERICHIA COLI K12 AT 2.0 A RESOLUTION CAVEAT 1YRR CHIRALITY ERROR AT CHIRAL CENTER CA OF MET 1 B COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GLCNAC 6-P DEACETYLASE; COMPND 5 EC: 3.5.1.25; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: NAGA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: IBPC 590; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PUC18 KEYWDS (BETA/ALPHA)8 BARREL, BETA SANDWICH, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.M.FERREIRA,R.APARICIO,G.MENDOZA-HERNANDEZ,M.L.CALCAGNO,G.OLIVA REVDAT 6 03-APR-24 1YRR 1 REMARK REVDAT 5 14-FEB-24 1YRR 1 REMARK REVDAT 4 13-JUL-11 1YRR 1 VERSN REVDAT 3 24-FEB-09 1YRR 1 VERSN REVDAT 2 03-OCT-06 1YRR 1 JRNL REVDAT 1 21-MAR-06 1YRR 0 JRNL AUTH F.M.FERREIRA,G.MENDOZA-HERNANDEZ,R.APARICIO,H.FISCHER, JRNL AUTH 2 M.L.CALCAGNO,G.OLIVA JRNL TITL STRUCTURAL ANALYSIS OF N-ACETYLGLUCOSAMINE-6-PHOSPHATE JRNL TITL 2 DEACETYLASE APOENZYME FROM ESCHERICHIA COLI. JRNL REF J.MOL.BIOL. V. 359 308 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16630633 JRNL DOI 10.1016/J.JMB.2006.03.024 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.M.FERREIRA,G.MENDOZA-HERNANDEZ,M.L.CALCAGNO,F.MINAURO, REMARK 1 AUTH 2 L.F.DELBONI,G.OLIVA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC ANALYSIS OF REMARK 1 TITL 2 N-ACETYLGLUCOSAMINE 6-PHOSPHATE DEACETYLASE FROM ESCHERICHIA REMARK 1 TITL 3 COLI REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 56 670 2000 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10771446 REMARK 1 DOI 10.1107/S0907444900003668 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 48144 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2540 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3618 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.1710 REMARK 3 BIN FREE R VALUE SET COUNT : 174 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5371 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 435 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.57000 REMARK 3 B22 (A**2) : -0.96000 REMARK 3 B33 (A**2) : 0.38000 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): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.204 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5550 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 5179 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7528 ; 1.887 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12043 ; 1.593 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 711 ; 7.751 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 892 ; 0.202 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6163 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1039 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1117 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5931 ; 0.249 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 3210 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 328 ; 0.169 ; 0.200 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): 23 ; 0.272 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 100 ; 0.320 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.308 ; 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): 3549 ; 1.091 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5709 ; 1.845 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2001 ; 2.837 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1819 ; 4.607 ; 4.500 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 : 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 : 1.40 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 1YRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031855. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-99; NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL; NULL REMARK 200 PH : 4.00 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; NULL; NULL REMARK 200 RADIATION SOURCE : LNLS; NULL; NULL REMARK 200 BEAMLINE : D03B-MX1; NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.378; NULL; NULL REMARK 200 MONOCHROMATOR : SI(111) CHANNEL CUT; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; NULL; NULL REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE; NULL; REMARK 200 NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50702 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.270 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELXD, SOLVE, RESOLVE REMARK 200 STARTING MODEL: EXPERIMENTAL PHASES FROM AN IODINE SOAKED CRYSTAL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM DIHYDROGENOPHOSPHATE HYDRATE, REMARK 280 PH 4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 4.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 41.07850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.27700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.07850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.27700 REMARK 290 SMTRY3 4 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HOMOTETRAMER HEXAMER GENERATED REMARK 300 FROM THE DIMER IN THE ASYMMETRIC UNIT 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: TETRAMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 82.15700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 601 LIES ON A SPECIAL POSITION. 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 GLY A 141 REMARK 465 MET B 1 REMARK 465 LEU B 137 REMARK 465 VAL B 138 REMARK 465 LYS B 139 REMARK 465 LYS B 140 REMARK 465 GLY B 141 REMARK 465 THR B 142 REMARK 465 HIS B 143 REMARK 465 ASN B 144 REMARK 465 PRO B 145 REMARK 465 ASN B 146 REMARK 465 PHE B 147 REMARK 465 VAL B 148 REMARK 465 ARG B 149 REMARK 465 LYS B 150 REMARK 465 PRO B 151 REMARK 465 ASP B 152 REMARK 465 ALA B 276 REMARK 465 PRO B 277 REMARK 465 ALA B 278 REMARK 465 GLY B 279 REMARK 465 ALA B 280 REMARK 465 ASN B 281 REMARK 465 ILE B 282 REMARK 465 GLU B 283 REMARK 465 GLN B 284 REMARK 465 PHE B 285 REMARK 465 ILE B 286 REMARK 465 PHE B 287 REMARK 465 ALA B 288 REMARK 465 GLY B 289 REMARK 465 LYS B 290 REMARK 465 THR B 291 REMARK 465 ILE B 292 REMARK 465 TYR B 293 REMARK 465 TYR B 294 REMARK 465 ARG B 295 REMARK 465 ASN B 296 REMARK 465 GLY B 297 REMARK 465 LEU B 298 REMARK 465 CYS B 299 REMARK 465 VAL B 300 REMARK 465 ASP B 301 REMARK 465 GLU B 302 REMARK 465 ASN B 303 REMARK 465 GLY B 304 REMARK 465 THR B 305 REMARK 465 LEU B 306 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 O2 GOL A 603 O HOH A 864 2.00 REMARK 500 O HOH A 839 O HOH A 842 2.06 REMARK 500 O ASN A 144 N ASN A 146 2.09 REMARK 500 O1 GOL A 602 O HOH A 865 2.15 REMARK 500 O HOH A 676 O HOH A 797 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH B 649 O HOH B 656 2655 1.70 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 VAL A 300 CB VAL A 300 CG1 -0.162 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 8 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 17 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 70 CB - CG - OD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 MET A 107 CG - SD - CE ANGL. DEV. = 11.8 DEGREES REMARK 500 ARG A 115 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 LEU A 130 CB - CG - CD2 ANGL. DEV. = -10.3 DEGREES REMARK 500 ASP A 152 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 157 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 164 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 MET A 221 CG - SD - CE ANGL. DEV. = -10.0 DEGREES REMARK 500 ARG A 348 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 348 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ASP B 70 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG B 262 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 262 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG B 318 NE - CZ - NH2 ANGL. DEV. = -3.1 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 GLU A 40 17.34 55.89 REMARK 500 ASP A 70 -42.92 74.96 REMARK 500 GLN A 124 -109.19 -128.88 REMARK 500 VAL A 138 -46.19 64.48 REMARK 500 LYS A 139 -143.80 -74.64 REMARK 500 HIS A 143 -68.44 -157.43 REMARK 500 ASN A 144 59.56 71.85 REMARK 500 PRO A 145 -7.17 -35.45 REMARK 500 HIS A 216 80.32 29.76 REMARK 500 TYR A 218 -27.48 86.77 REMARK 500 ALA A 247 54.29 -100.73 REMARK 500 ALA A 288 46.71 34.76 REMARK 500 THR A 336 -82.11 -141.25 REMARK 500 GLU B 40 -0.02 72.58 REMARK 500 ASN B 69 -169.53 173.46 REMARK 500 ASP B 70 -68.88 69.93 REMARK 500 THR B 71 -145.66 -102.46 REMARK 500 GLN B 124 -111.55 -134.88 REMARK 500 HIS B 216 78.68 38.57 REMARK 500 TYR B 218 -35.06 83.21 REMARK 500 ALA B 247 52.53 -105.27 REMARK 500 THR B 336 -84.43 -136.88 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 THR A 142 HIS A 143 -149.96 REMARK 500 HIS A 143 ASN A 144 -144.74 REMARK 500 ARG A 295 ASN A 296 -73.48 REMARK 500 PHE B 68 ASN B 69 -146.80 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 PO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 603 DBREF 1YRR A 1 382 UNP P15300 NAGA_ECOLI 1 382 DBREF 1YRR B 1 382 UNP P15300 NAGA_ECOLI 1 382 SEQRES 1 A 382 MET TYR ALA LEU THR GLN GLY ARG ILE PHE THR GLY HIS SEQRES 2 A 382 GLU PHE LEU ASP ASP HIS ALA VAL VAL ILE ALA ASP GLY SEQRES 3 A 382 LEU ILE LYS SER VAL CYS PRO VAL ALA GLU LEU PRO PRO SEQRES 4 A 382 GLU ILE GLU GLN ARG SER LEU ASN GLY ALA ILE LEU SER SEQRES 5 A 382 PRO GLY PHE ILE ASP VAL GLN LEU ASN GLY CYS GLY GLY SEQRES 6 A 382 VAL GLN PHE ASN ASP THR ALA GLU ALA VAL SER VAL GLU SEQRES 7 A 382 THR LEU GLU ILE MET GLN LYS ALA ASN GLU LYS SER GLY SEQRES 8 A 382 CYS THR ASN TYR LEU PRO THR LEU ILE THR THR SER ASP SEQRES 9 A 382 GLU LEU MET LYS GLN GLY VAL ARG VAL MET ARG GLU TYR SEQRES 10 A 382 LEU ALA LYS HIS PRO ASN GLN ALA LEU GLY LEU HIS LEU SEQRES 11 A 382 GLU GLY PRO TRP LEU ASN LEU VAL LYS LYS GLY THR HIS SEQRES 12 A 382 ASN PRO ASN PHE VAL ARG LYS PRO ASP ALA ALA LEU VAL SEQRES 13 A 382 ASP PHE LEU CYS GLU ASN ALA ASP VAL ILE THR LYS VAL SEQRES 14 A 382 THR LEU ALA PRO GLU MET VAL PRO ALA GLU VAL ILE SER SEQRES 15 A 382 LYS LEU ALA ASN ALA GLY ILE VAL VAL SER ALA GLY HIS SEQRES 16 A 382 SER ASN ALA THR LEU LYS GLU ALA LYS ALA GLY PHE ARG SEQRES 17 A 382 ALA GLY ILE THR PHE ALA THR HIS LEU TYR ASN ALA MET SEQRES 18 A 382 PRO TYR ILE THR GLY ARG GLU PRO GLY LEU ALA GLY ALA SEQRES 19 A 382 ILE LEU ASP GLU ALA ASP ILE TYR CYS GLY ILE ILE ALA SEQRES 20 A 382 ASP GLY LEU HIS VAL ASP TYR ALA ASN ILE ARG ASN ALA SEQRES 21 A 382 LYS ARG LEU LYS GLY ASP LYS LEU CYS LEU VAL THR ASP SEQRES 22 A 382 ALA THR ALA PRO ALA GLY ALA ASN ILE GLU GLN PHE ILE SEQRES 23 A 382 PHE ALA GLY LYS THR ILE TYR TYR ARG ASN GLY LEU CYS SEQRES 24 A 382 VAL ASP GLU ASN GLY THR LEU SER GLY SER SER LEU THR SEQRES 25 A 382 MET ILE GLU GLY VAL ARG ASN LEU VAL GLU HIS CYS GLY SEQRES 26 A 382 ILE ALA LEU ASP GLU VAL LEU ARG MET ALA THR LEU TYR SEQRES 27 A 382 PRO ALA ARG ALA ILE GLY VAL GLU LYS ARG LEU GLY THR SEQRES 28 A 382 LEU ALA ALA GLY LYS VAL ALA ASN LEU THR ALA PHE THR SEQRES 29 A 382 PRO ASP PHE LYS ILE THR LYS THR ILE VAL ASN GLY ASN SEQRES 30 A 382 GLU VAL VAL THR GLN SEQRES 1 B 382 MET TYR ALA LEU THR GLN GLY ARG ILE PHE THR GLY HIS SEQRES 2 B 382 GLU PHE LEU ASP ASP HIS ALA VAL VAL ILE ALA ASP GLY SEQRES 3 B 382 LEU ILE LYS SER VAL CYS PRO VAL ALA GLU LEU PRO PRO SEQRES 4 B 382 GLU ILE GLU GLN ARG SER LEU ASN GLY ALA ILE LEU SER SEQRES 5 B 382 PRO GLY PHE ILE ASP VAL GLN LEU ASN GLY CYS GLY GLY SEQRES 6 B 382 VAL GLN PHE ASN ASP THR ALA GLU ALA VAL SER VAL GLU SEQRES 7 B 382 THR LEU GLU ILE MET GLN LYS ALA ASN GLU LYS SER GLY SEQRES 8 B 382 CYS THR ASN TYR LEU PRO THR LEU ILE THR THR SER ASP SEQRES 9 B 382 GLU LEU MET LYS GLN GLY VAL ARG VAL MET ARG GLU TYR SEQRES 10 B 382 LEU ALA LYS HIS PRO ASN GLN ALA LEU GLY LEU HIS LEU SEQRES 11 B 382 GLU GLY PRO TRP LEU ASN LEU VAL LYS LYS GLY THR HIS SEQRES 12 B 382 ASN PRO ASN PHE VAL ARG LYS PRO ASP ALA ALA LEU VAL SEQRES 13 B 382 ASP PHE LEU CYS GLU ASN ALA ASP VAL ILE THR LYS VAL SEQRES 14 B 382 THR LEU ALA PRO GLU MET VAL PRO ALA GLU VAL ILE SER SEQRES 15 B 382 LYS LEU ALA ASN ALA GLY ILE VAL VAL SER ALA GLY HIS SEQRES 16 B 382 SER ASN ALA THR LEU LYS GLU ALA LYS ALA GLY PHE ARG SEQRES 17 B 382 ALA GLY ILE THR PHE ALA THR HIS LEU TYR ASN ALA MET SEQRES 18 B 382 PRO TYR ILE THR GLY ARG GLU PRO GLY LEU ALA GLY ALA SEQRES 19 B 382 ILE LEU ASP GLU ALA ASP ILE TYR CYS GLY ILE ILE ALA SEQRES 20 B 382 ASP GLY LEU HIS VAL ASP TYR ALA ASN ILE ARG ASN ALA SEQRES 21 B 382 LYS ARG LEU LYS GLY ASP LYS LEU CYS LEU VAL THR ASP SEQRES 22 B 382 ALA THR ALA PRO ALA GLY ALA ASN ILE GLU GLN PHE ILE SEQRES 23 B 382 PHE ALA GLY LYS THR ILE TYR TYR ARG ASN GLY LEU CYS SEQRES 24 B 382 VAL ASP GLU ASN GLY THR LEU SER GLY SER SER LEU THR SEQRES 25 B 382 MET ILE GLU GLY VAL ARG ASN LEU VAL GLU HIS CYS GLY SEQRES 26 B 382 ILE ALA LEU ASP GLU VAL LEU ARG MET ALA THR LEU TYR SEQRES 27 B 382 PRO ALA ARG ALA ILE GLY VAL GLU LYS ARG LEU GLY THR SEQRES 28 B 382 LEU ALA ALA GLY LYS VAL ALA ASN LEU THR ALA PHE THR SEQRES 29 B 382 PRO ASP PHE LYS ILE THR LYS THR ILE VAL ASN GLY ASN SEQRES 30 B 382 GLU VAL VAL THR GLN HET PO4 A 501 5 HET GOL A 601 6 HET GOL A 602 6 HET GOL A 603 6 HET PO4 B 502 5 HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 PO4 2(O4 P 3-) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 8 HOH *435(H2 O) HELIX 1 1 ALA A 35 LEU A 37 5 3 HELIX 2 2 SER A 76 SER A 90 1 15 HELIX 3 3 SER A 103 HIS A 121 1 19 HELIX 4 4 ARG A 149 ASN A 162 1 14 HELIX 5 5 ALA A 172 VAL A 176 5 5 HELIX 6 6 PRO A 177 ALA A 187 1 11 HELIX 7 7 THR A 199 GLY A 210 1 12 HELIX 8 8 PRO A 229 GLU A 238 1 10 HELIX 9 9 ASP A 253 GLY A 265 1 13 HELIX 10 10 THR A 312 GLY A 325 1 14 HELIX 11 11 ALA A 327 THR A 336 1 10 HELIX 12 12 THR A 336 ILE A 343 1 8 HELIX 13 13 ALA B 35 LEU B 37 5 3 HELIX 14 14 SER B 76 LYS B 89 1 14 HELIX 15 15 SER B 103 HIS B 121 1 19 HELIX 16 16 ALA B 153 ASN B 162 1 10 HELIX 17 17 ALA B 172 VAL B 176 5 5 HELIX 18 18 PRO B 177 GLY B 188 1 12 HELIX 19 19 THR B 199 GLY B 210 1 12 HELIX 20 20 PRO B 229 GLU B 238 1 10 HELIX 21 21 ASP B 253 GLY B 265 1 13 HELIX 22 22 THR B 312 GLY B 325 1 14 HELIX 23 23 ALA B 327 THR B 336 1 10 HELIX 24 24 THR B 336 ILE B 343 1 8 SHEET 1 A 4 LEU A 27 PRO A 33 0 SHEET 2 A 4 HIS A 19 ALA A 24 -1 N VAL A 22 O SER A 30 SHEET 3 A 4 TYR A 2 THR A 5 -1 N TYR A 2 O ILE A 23 SHEET 4 A 4 GLU A 42 SER A 45 1 O ARG A 44 N ALA A 3 SHEET 1 B 6 PHE A 15 LEU A 16 0 SHEET 2 B 6 ARG A 8 PHE A 10 -1 N ILE A 9 O LEU A 16 SHEET 3 B 6 ILE A 50 PRO A 53 1 O LEU A 51 N PHE A 10 SHEET 4 B 6 LEU A 360 PHE A 363 -1 O THR A 361 N SER A 52 SHEET 5 B 6 ILE A 369 VAL A 374 -1 O ILE A 373 N LEU A 360 SHEET 6 B 6 ASN A 377 THR A 381 -1 O VAL A 379 N THR A 372 SHEET 1 C 8 PHE A 55 LEU A 60 0 SHEET 2 C 8 CYS A 92 ILE A 100 1 O ASN A 94 N ASP A 57 SHEET 3 C 8 LEU A 128 GLU A 131 1 O HIS A 129 N PRO A 97 SHEET 4 C 8 ILE A 166 LEU A 171 1 O LYS A 168 N LEU A 130 SHEET 5 C 8 VAL A 190 ALA A 193 1 O SER A 192 N VAL A 169 SHEET 6 C 8 PHE A 213 ALA A 214 1 O PHE A 213 N ALA A 193 SHEET 7 C 8 TYR A 242 ILE A 246 1 O GLY A 244 N ALA A 214 SHEET 8 C 8 LEU A 268 VAL A 271 1 O CYS A 269 N CYS A 243 SHEET 1 D 2 GLY A 62 CYS A 63 0 SHEET 2 D 2 VAL A 66 GLN A 67 -1 O VAL A 66 N CYS A 63 SHEET 1 E 4 GLN A 284 PHE A 287 0 SHEET 2 E 4 LYS A 290 TYR A 294 -1 O ILE A 292 N PHE A 285 SHEET 3 E 4 CYS A 299 VAL A 300 -1 O VAL A 300 N TYR A 293 SHEET 4 E 4 LEU A 306 GLY A 308 -1 O SER A 307 N CYS A 299 SHEET 1 F 4 LEU B 27 PRO B 33 0 SHEET 2 F 4 HIS B 19 ALA B 24 -1 N ALA B 24 O LEU B 27 SHEET 3 F 4 TYR B 2 THR B 5 -1 N TYR B 2 O ILE B 23 SHEET 4 F 4 GLN B 43 SER B 45 1 O ARG B 44 N ALA B 3 SHEET 1 G 6 PHE B 15 LEU B 16 0 SHEET 2 G 6 ARG B 8 PHE B 10 -1 N ILE B 9 O LEU B 16 SHEET 3 G 6 ILE B 50 PRO B 53 1 O LEU B 51 N PHE B 10 SHEET 4 G 6 LEU B 360 PHE B 363 -1 O PHE B 363 N ILE B 50 SHEET 5 G 6 ILE B 369 VAL B 374 -1 O ILE B 373 N LEU B 360 SHEET 6 G 6 ASN B 377 THR B 381 -1 O ASN B 377 N VAL B 374 SHEET 1 H 8 PHE B 55 LEU B 60 0 SHEET 2 H 8 CYS B 92 LEU B 99 1 O ASN B 94 N ASP B 57 SHEET 3 H 8 LEU B 128 GLU B 131 1 O HIS B 129 N LEU B 99 SHEET 4 H 8 ILE B 166 LEU B 171 1 O LYS B 168 N LEU B 130 SHEET 5 H 8 VAL B 190 ALA B 193 1 O VAL B 190 N THR B 167 SHEET 6 H 8 ILE B 211 ALA B 214 1 O PHE B 213 N ALA B 193 SHEET 7 H 8 TYR B 242 ILE B 246 1 O TYR B 242 N THR B 212 SHEET 8 H 8 LEU B 268 VAL B 271 1 O CYS B 269 N CYS B 243 SHEET 1 I 2 GLY B 62 CYS B 63 0 SHEET 2 I 2 VAL B 66 GLN B 67 -1 O VAL B 66 N CYS B 63 CISPEP 1 GLY A 132 PRO A 133 0 -5.21 CISPEP 2 GLY B 132 PRO B 133 0 -1.78 SITE 1 AC1 7 GLN A 59 GLU A 131 HIS A 195 HIS A 216 SITE 2 AC1 7 ASP A 273 HOH A 858 HOH A 860 SITE 1 AC2 6 ASN B 61 GLU B 131 HIS B 195 HIS B 216 SITE 2 AC2 6 ASP B 273 HOH B 672 SITE 1 AC3 5 THR A 225 GLY A 226 ARG A 227 GLU A 228 SITE 2 AC3 5 TYR B 223 SITE 1 AC4 8 ASP A 253 ALA A 255 ARG A 258 HIS A 323 SITE 2 AC4 8 HOH A 862 HOH A 865 HOH A 866 LEU B 200 SITE 1 AC5 5 LYS A 261 ARG A 262 GLY A 265 HOH A 863 SITE 2 AC5 5 HOH A 864 CRYST1 82.157 114.554 80.208 90.00 90.00 90.00 P 21 21 2 8 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 0.012172 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012468 0.00000