HEADER HYDROLASE 10-APR-05 1ZC2 TITLE CRYSTAL STRUCTURE OF PLASMID-ENCODED CLASS C BETA-LACTAMASE CMY-2 TITLE 2 COMPLEXED WITH CITRATE MOLECULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE CLASS C; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-361; COMPND 5 SYNONYM: CMY-2 BETA-LACTAMASE; COMPND 6 EC: 3.5.2.6; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLA CMY-2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET26B(+) KEYWDS BETA-LACTAMASE CEPHALOSPORINASE, AMPC-TYPE, SERINE HYDROLASE, KEYWDS 2 CITRATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.BAUVOIS,L.JACQUAMET,S.FIEULAINE,J.-M.FRERE,M.GALLENI,J.-L.FERRER REVDAT 3 13-MAR-24 1ZC2 1 REMARK REVDAT 2 24-FEB-09 1ZC2 1 VERSN REVDAT 1 25-APR-06 1ZC2 0 JRNL AUTH C.BAUVOIS,L.JACQUAMET,S.FIEULAINE,J.-M.FRERE,M.GALLENI, JRNL AUTH 2 J.-L.FERRER JRNL TITL CRYSTALLOGRAPHIC STRUCTURE OF PLASMID-ENCODED CMY-2 JRNL TITL 2 BETA-LACTAMASE REVEALED CITRATE MOLECULE IN THE ACTIVE SITE. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43482 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2170 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) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2699 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5562 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 445 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.03000 REMARK 3 B22 (A**2) : 2.39000 REMARK 3 B33 (A**2) : -1.36000 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): 0.284 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.198 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.538 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5740 ; 0.036 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7832 ; 2.752 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 712 ; 7.710 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 243 ;38.682 ;24.486 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 912 ;20.648 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;27.451 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 843 ; 0.188 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4407 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3111 ; 0.284 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3782 ; 0.322 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 455 ; 0.229 ; 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): 42 ; 0.214 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.262 ; 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): 3729 ; 1.927 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5715 ; 2.305 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2504 ; 4.214 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2117 ; 5.623 ; 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 : 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 1ZC2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032551. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 4.0 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) : 0.979565 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43482 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 43.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CITRIC ACID 0.1M, PEG 6000 30 % W/V, REMARK 280 PH 4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 36.35500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.65500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.65500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.35500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.55000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ALA A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 ALA B 1 REMARK 465 ALA B 2 REMARK 465 LYS B 3 REMARK 465 THR B 4 REMARK 465 GLU B 5 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 B 6 CG CD OE1 NE2 REMARK 470 ARG B 14 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 207 CG CD CE NZ REMARK 470 LYS B 279 CG CD CE NZ 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 OE2 GLU A 82 NH2 ARG A 177 2.14 REMARK 500 O HOH A 619 O HOH A 719 2.16 REMARK 500 CB VAL B 54 O HOH B 693 2.17 REMARK 500 O HOH A 674 O HOH A 713 2.18 REMARK 500 O HOH B 635 O HOH B 716 2.18 REMARK 500 OG SER B 64 OH TYR B 150 2.18 REMARK 500 O HOH B 515 O HOH B 634 2.19 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 ALA A 29 CA ALA A 29 CB -0.133 REMARK 500 LYS A 37 CD LYS A 37 CE 0.174 REMARK 500 LYS A 45 CE LYS A 45 NZ 0.163 REMARK 500 ASN A 50 CB ASN A 50 CG 0.202 REMARK 500 VAL A 65 CA VAL A 65 CB 0.237 REMARK 500 THR A 68 CA THR A 68 CB 0.160 REMARK 500 GLU A 82 CD GLU A 82 OE1 0.070 REMARK 500 PHE A 158 CG PHE A 158 CD1 0.099 REMARK 500 GLU A 172 C GLU A 172 O 0.115 REMARK 500 TYR A 199 CE2 TYR A 199 CD2 0.093 REMARK 500 TRP A 233 CE3 TRP A 233 CZ3 -0.105 REMARK 500 VAL A 243 CB VAL A 243 CG1 0.146 REMARK 500 TYR A 266 CZ TYR A 266 CE2 0.085 REMARK 500 GLY A 321 C GLY A 321 O 0.104 REMARK 500 VAL A 326 CB VAL A 326 CG2 0.161 REMARK 500 TYR A 344 CE1 TYR A 344 CZ 0.090 REMARK 500 VAL B 54 CB VAL B 54 CG2 0.136 REMARK 500 PHE B 69 CE2 PHE B 69 CD2 0.165 REMARK 500 ALA B 79 CA ALA B 79 CB -0.156 REMARK 500 TYR B 170 CE2 TYR B 170 CD2 0.116 REMARK 500 GLU B 171 CD GLU B 171 OE1 0.088 REMARK 500 LYS B 224 CE LYS B 224 NZ 0.275 REMARK 500 GLN B 250 CB GLN B 250 CG 0.164 REMARK 500 TYR B 266 CG TYR B 266 CD2 0.091 REMARK 500 VAL B 308 CB VAL B 308 CG1 -0.162 REMARK 500 VAL B 313 CB VAL B 313 CG1 0.164 REMARK 500 TYR B 325 CZ TYR B 325 CE2 -0.082 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 LEU A 62 CB - CG - CD1 ANGL. DEV. = 16.9 DEGREES REMARK 500 LEU A 62 CB - CG - CD2 ANGL. DEV. = -10.8 DEGREES REMARK 500 GLY A 98 C - N - CA ANGL. DEV. = -14.1 DEGREES REMARK 500 ASP A 127 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 148 CG - CD - NE ANGL. DEV. = -13.6 DEGREES REMARK 500 ARG A 148 CD - NE - CZ ANGL. DEV. = 11.8 DEGREES REMARK 500 ARG A 148 NE - CZ - NH1 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG A 148 NE - CZ - NH2 ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 177 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 VAL A 178 CG1 - CB - CG2 ANGL. DEV. = -13.8 DEGREES REMARK 500 LEU A 184 CB - CG - CD1 ANGL. DEV. = 10.7 DEGREES REMARK 500 ASP A 217 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 LEU A 248 CB - CG - CD1 ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 258 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 LEU A 274 CA - CB - CG ANGL. DEV. = 16.8 DEGREES REMARK 500 ARG A 349 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP B 47 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 VAL B 54 CB - CA - C ANGL. DEV. = -12.3 DEGREES REMARK 500 LEU B 62 CB - CG - CD1 ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG B 148 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 LEU B 161 CB - CG - CD1 ANGL. DEV. = -13.3 DEGREES REMARK 500 LEU B 161 CB - CG - CD2 ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG B 176 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG B 177 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG B 177 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ASP B 217 CB - CG - OD2 ANGL. DEV. = 9.3 DEGREES REMARK 500 VAL B 227 CB - CA - C ANGL. DEV. = -11.5 DEGREES REMARK 500 ARG B 232 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG B 258 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 261 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 MET B 273 CB - CG - SD ANGL. DEV. = 19.3 DEGREES REMARK 500 ASP B 288 CB - CG - OD2 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 349 NE - CZ - NH2 ANGL. DEV. = -4.7 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 SER A 154 -70.13 -96.22 REMARK 500 TYR A 221 18.89 -166.08 REMARK 500 ASN A 341 45.93 -91.79 REMARK 500 LEU A 360 22.13 -151.31 REMARK 500 SER B 64 -6.29 -57.09 REMARK 500 SER B 66 -28.82 -39.77 REMARK 500 TRP B 93 67.67 -153.96 REMARK 500 LYS B 183 40.57 74.69 REMARK 500 TYR B 221 8.70 -158.71 REMARK 500 ASN B 341 45.42 -95.50 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 CIT A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 502 DBREF 1ZC2 A 1 361 UNP Q48434 Q48434_KLEPN 21 381 DBREF 1ZC2 B 1 361 UNP Q48434 Q48434_KLEPN 21 381 SEQRES 1 A 361 ALA ALA LYS THR GLU GLN GLN ILE ALA ASP ILE VAL ASN SEQRES 2 A 361 ARG THR ILE THR PRO LEU MET GLN GLU GLN ALA ILE PRO SEQRES 3 A 361 GLY MET ALA VAL ALA VAL ILE TYR GLN GLY LYS PRO TYR SEQRES 4 A 361 TYR PHE THR TRP GLY LYS ALA ASP ILE ALA ASN ASN HIS SEQRES 5 A 361 PRO VAL THR GLN GLN THR LEU PHE GLU LEU GLY SER VAL SEQRES 6 A 361 SER LYS THR PHE ASN GLY VAL LEU GLY GLY ASP ALA ILE SEQRES 7 A 361 ALA ARG GLY GLU ILE LYS LEU SER ASP PRO VAL THR LYS SEQRES 8 A 361 TYR TRP PRO GLU LEU THR GLY LYS GLN TRP GLN GLY ILE SEQRES 9 A 361 ARG LEU LEU HIS LEU ALA THR TYR THR ALA GLY GLY LEU SEQRES 10 A 361 PRO LEU GLN ILE PRO ASP ASP VAL ARG ASP LYS ALA ALA SEQRES 11 A 361 LEU LEU HIS PHE TYR GLN ASN TRP GLN PRO GLN TRP THR SEQRES 12 A 361 PRO GLY ALA LYS ARG LEU TYR ALA ASN SER SER ILE GLY SEQRES 13 A 361 LEU PHE GLY ALA LEU ALA VAL LYS PRO SER GLY MET SER SEQRES 14 A 361 TYR GLU GLU ALA MET THR ARG ARG VAL LEU GLN PRO LEU SEQRES 15 A 361 LYS LEU ALA HIS THR TRP ILE THR VAL PRO GLN ASN GLU SEQRES 16 A 361 GLN LYS ASP TYR ALA TRP GLY TYR ARG GLU GLY LYS PRO SEQRES 17 A 361 VAL HIS VAL SER PRO GLY GLN LEU ASP ALA GLU ALA TYR SEQRES 18 A 361 GLY VAL LYS SER SER VAL ILE ASP MET ALA ARG TRP VAL SEQRES 19 A 361 GLN ALA ASN MET ASP ALA SER HIS VAL GLN GLU LYS THR SEQRES 20 A 361 LEU GLN GLN GLY ILE ALA LEU ALA GLN SER ARG TYR TRP SEQRES 21 A 361 ARG ILE GLY ASP MET TYR GLN GLY LEU GLY TRP GLU MET SEQRES 22 A 361 LEU ASN TRP PRO LEU LYS ALA ASP SER ILE ILE ASN GLY SEQRES 23 A 361 SER ASP SER LYS VAL ALA LEU ALA ALA LEU PRO ALA VAL SEQRES 24 A 361 GLU VAL ASN PRO PRO ALA PRO ALA VAL LYS ALA SER TRP SEQRES 25 A 361 VAL HIS LYS THR GLY SER THR GLY GLY PHE GLY SER TYR SEQRES 26 A 361 VAL ALA PHE VAL PRO GLU LYS ASN LEU GLY ILE VAL MET SEQRES 27 A 361 LEU ALA ASN LYS SER TYR PRO ASN PRO VAL ARG VAL GLU SEQRES 28 A 361 ALA ALA TRP ARG ILE LEU GLU LYS LEU GLN SEQRES 1 B 361 ALA ALA LYS THR GLU GLN GLN ILE ALA ASP ILE VAL ASN SEQRES 2 B 361 ARG THR ILE THR PRO LEU MET GLN GLU GLN ALA ILE PRO SEQRES 3 B 361 GLY MET ALA VAL ALA VAL ILE TYR GLN GLY LYS PRO TYR SEQRES 4 B 361 TYR PHE THR TRP GLY LYS ALA ASP ILE ALA ASN ASN HIS SEQRES 5 B 361 PRO VAL THR GLN GLN THR LEU PHE GLU LEU GLY SER VAL SEQRES 6 B 361 SER LYS THR PHE ASN GLY VAL LEU GLY GLY ASP ALA ILE SEQRES 7 B 361 ALA ARG GLY GLU ILE LYS LEU SER ASP PRO VAL THR LYS SEQRES 8 B 361 TYR TRP PRO GLU LEU THR GLY LYS GLN TRP GLN GLY ILE SEQRES 9 B 361 ARG LEU LEU HIS LEU ALA THR TYR THR ALA GLY GLY LEU SEQRES 10 B 361 PRO LEU GLN ILE PRO ASP ASP VAL ARG ASP LYS ALA ALA SEQRES 11 B 361 LEU LEU HIS PHE TYR GLN ASN TRP GLN PRO GLN TRP THR SEQRES 12 B 361 PRO GLY ALA LYS ARG LEU TYR ALA ASN SER SER ILE GLY SEQRES 13 B 361 LEU PHE GLY ALA LEU ALA VAL LYS PRO SER GLY MET SER SEQRES 14 B 361 TYR GLU GLU ALA MET THR ARG ARG VAL LEU GLN PRO LEU SEQRES 15 B 361 LYS LEU ALA HIS THR TRP ILE THR VAL PRO GLN ASN GLU SEQRES 16 B 361 GLN LYS ASP TYR ALA TRP GLY TYR ARG GLU GLY LYS PRO SEQRES 17 B 361 VAL HIS VAL SER PRO GLY GLN LEU ASP ALA GLU ALA TYR SEQRES 18 B 361 GLY VAL LYS SER SER VAL ILE ASP MET ALA ARG TRP VAL SEQRES 19 B 361 GLN ALA ASN MET ASP ALA SER HIS VAL GLN GLU LYS THR SEQRES 20 B 361 LEU GLN GLN GLY ILE ALA LEU ALA GLN SER ARG TYR TRP SEQRES 21 B 361 ARG ILE GLY ASP MET TYR GLN GLY LEU GLY TRP GLU MET SEQRES 22 B 361 LEU ASN TRP PRO LEU LYS ALA ASP SER ILE ILE ASN GLY SEQRES 23 B 361 SER ASP SER LYS VAL ALA LEU ALA ALA LEU PRO ALA VAL SEQRES 24 B 361 GLU VAL ASN PRO PRO ALA PRO ALA VAL LYS ALA SER TRP SEQRES 25 B 361 VAL HIS LYS THR GLY SER THR GLY GLY PHE GLY SER TYR SEQRES 26 B 361 VAL ALA PHE VAL PRO GLU LYS ASN LEU GLY ILE VAL MET SEQRES 27 B 361 LEU ALA ASN LYS SER TYR PRO ASN PRO VAL ARG VAL GLU SEQRES 28 B 361 ALA ALA TRP ARG ILE LEU GLU LYS LEU GLN HET CIT A 501 13 HET CIT B 502 13 HETNAM CIT CITRIC ACID FORMUL 3 CIT 2(C6 H8 O7) FORMUL 5 HOH *445(H2 O) HELIX 1 1 THR A 4 ALA A 24 1 21 HELIX 2 2 VAL A 65 GLY A 81 1 17 HELIX 3 3 GLY A 98 GLN A 102 5 5 HELIX 4 4 ARG A 105 THR A 111 1 7 HELIX 5 5 ASP A 127 TRP A 138 1 12 HELIX 6 6 ALA A 151 VAL A 163 1 13 HELIX 7 7 LYS A 164 GLY A 167 5 4 HELIX 8 8 SER A 169 VAL A 178 1 10 HELIX 9 9 PRO A 192 TYR A 199 5 8 HELIX 10 10 LEU A 216 TYR A 221 1 6 HELIX 11 11 SER A 226 ASP A 239 1 14 HELIX 12 12 GLU A 245 GLN A 256 1 12 HELIX 13 13 LYS A 279 SER A 287 1 9 HELIX 14 14 ASP A 288 LEU A 293 1 6 HELIX 15 15 PRO A 330 ASN A 333 5 4 HELIX 16 16 PRO A 345 LYS A 359 1 15 HELIX 17 17 GLN B 6 ALA B 24 1 19 HELIX 18 18 VAL B 65 ARG B 80 1 16 HELIX 19 19 VAL B 89 TRP B 93 5 5 HELIX 20 20 GLY B 98 GLN B 102 5 5 HELIX 21 21 ARG B 105 THR B 111 1 7 HELIX 22 22 ASP B 127 TRP B 138 1 12 HELIX 23 23 ALA B 151 VAL B 163 1 13 HELIX 24 24 LYS B 164 GLY B 167 5 4 HELIX 25 25 SER B 169 VAL B 178 1 10 HELIX 26 26 VAL B 178 LYS B 183 1 6 HELIX 27 27 GLU B 195 TYR B 199 5 5 HELIX 28 28 LEU B 216 TYR B 221 1 6 HELIX 29 29 SER B 226 ASP B 239 1 14 HELIX 30 30 GLU B 245 SER B 257 1 13 HELIX 31 31 LYS B 279 SER B 287 1 9 HELIX 32 32 ASP B 288 LEU B 293 1 6 HELIX 33 33 PRO B 345 LYS B 359 1 15 SHEET 1 A10 HIS A 52 PRO A 53 0 SHEET 2 A10 LYS A 37 ASP A 47 -1 N ALA A 46 O HIS A 52 SHEET 3 A10 GLY A 27 TYR A 34 -1 N MET A 28 O TRP A 43 SHEET 4 A10 GLY A 335 ALA A 340 -1 O VAL A 337 N ALA A 31 SHEET 5 A10 GLY A 323 PHE A 328 -1 N ALA A 327 O ILE A 336 SHEET 6 A10 SER A 311 SER A 318 -1 N VAL A 313 O PHE A 328 SHEET 7 A10 GLU A 272 ASN A 275 -1 N LEU A 274 O TRP A 312 SHEET 8 A10 MET A 265 GLN A 267 -1 N TYR A 266 O MET A 273 SHEET 9 A10 ARG A 258 ILE A 262 -1 N ILE A 262 O MET A 265 SHEET 10 A10 VAL A 299 ALA A 305 -1 O VAL A 299 N ARG A 261 SHEET 1 B 3 PHE A 60 GLU A 61 0 SHEET 2 B 3 LYS A 224 SER A 225 -1 O SER A 225 N PHE A 60 SHEET 3 B 3 THR A 187 TRP A 188 -1 N TRP A 188 O LYS A 224 SHEET 1 C 2 LYS A 147 ARG A 148 0 SHEET 2 C 2 LEU A 296 PRO A 297 -1 O LEU A 296 N ARG A 148 SHEET 1 D 2 GLY A 202 ARG A 204 0 SHEET 2 D 2 LYS A 207 VAL A 209 -1 O VAL A 209 N GLY A 202 SHEET 1 E10 HIS B 52 PRO B 53 0 SHEET 2 E10 LYS B 37 ASP B 47 -1 N ASP B 47 O HIS B 52 SHEET 3 E10 GLY B 27 TYR B 34 -1 N MET B 28 O TRP B 43 SHEET 4 E10 LEU B 334 ALA B 340 -1 O GLY B 335 N ILE B 33 SHEET 5 E10 GLY B 323 PHE B 328 -1 N ALA B 327 O ILE B 336 SHEET 6 E10 SER B 311 SER B 318 -1 N VAL B 313 O PHE B 328 SHEET 7 E10 GLU B 272 ASN B 275 -1 N LEU B 274 O TRP B 312 SHEET 8 E10 MET B 265 GLN B 267 -1 N TYR B 266 O MET B 273 SHEET 9 E10 ARG B 258 ILE B 262 -1 N ILE B 262 O MET B 265 SHEET 10 E10 VAL B 299 ALA B 305 -1 O VAL B 301 N TYR B 259 SHEET 1 F 3 PHE B 60 GLU B 61 0 SHEET 2 F 3 LYS B 224 SER B 225 -1 O SER B 225 N PHE B 60 SHEET 3 F 3 THR B 187 TRP B 188 -1 N TRP B 188 O LYS B 224 SHEET 1 G 2 LYS B 147 ARG B 148 0 SHEET 2 G 2 LEU B 296 PRO B 297 -1 O LEU B 296 N ARG B 148 SHEET 1 H 2 GLY B 202 ARG B 204 0 SHEET 2 H 2 LYS B 207 VAL B 209 -1 O VAL B 209 N GLY B 202 CISPEP 1 TRP A 276 PRO A 277 0 12.96 CISPEP 2 ASN A 302 PRO A 303 0 5.45 CISPEP 3 TRP B 276 PRO B 277 0 5.47 CISPEP 4 ASN B 302 PRO B 303 0 -12.51 SITE 1 AC1 13 SER A 64 TYR A 150 ALA A 292 LYS A 315 SITE 2 AC1 13 THR A 316 GLY A 317 SER A 318 ASN A 346 SITE 3 AC1 13 HOH A 528 HOH A 531 HOH A 564 HOH A 597 SITE 4 AC1 13 HOH B 618 SITE 1 AC2 14 HOH A 656 SER B 64 TYR B 150 ALA B 292 SITE 2 AC2 14 LYS B 315 GLY B 317 SER B 318 ASN B 346 SITE 3 AC2 14 ARG B 349 HOH B 517 HOH B 537 HOH B 670 SITE 4 AC2 14 HOH B 714 HOH B 719 CRYST1 72.710 97.100 103.310 90.00 90.00 90.00 P 21 21 21 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 0.013753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010299 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009680 0.00000