HEADER HYDROLASE 29-OCT-09 3KGM OBSLTE 27-JUL-11 3KGM 3SH7 TITLE CRYSTAL STRUCTURE OF FLUOROPHORE-LABELED CLASS A BETA-LACTAMASE PENP- TITLE 2 E166CB CAVEAT 3KGM CHIRALITY ERROR AT CA CENTER OF GLU B 168 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 47-303; COMPND 5 SYNONYM: PENICILLINASE, LARGE EXOPENICILLINASE, SMALL COMPND 6 EXOPENICILLINASE; COMPND 7 EC: 3.5.2.6; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 ORGANISM_TAXID: 1402; SOURCE 4 STRAIN: 749/C; SOURCE 5 GENE: BLAP, PENP; 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: PRSET KEYWDS BETA-LACTAMASE, FLUOROPHORE, BIOSENSOR, HYDROLASE, ANTIBIOTIC KEYWDS 2 RESISTANCE, CELL MEMBRANE, LIPOPROTEIN, MEMBRANE, PALMITATE EXPDTA X-RAY DIFFRACTION AUTHOR W.T.WONG REVDAT 2 27-JUL-11 3KGM 1 OBSLTE REVDAT 1 08-DEC-10 3KGM 0 JRNL AUTH W.T.WONG JRNL TITL CRYSTAL STRUCTURE OF FLUOROPHORE-LABELED CLASS A JRNL TITL 2 BETA-LACTAMASE PENP-E166CB JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16654 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 901 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1229 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.1750 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4011 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 351 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.19000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.335 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.220 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.508 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.861 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4093 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5531 ; 2.319 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 503 ;14.901 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 186 ;37.549 ;24.946 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 740 ;19.521 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;19.787 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 637 ; 0.381 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3040 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2015 ; 0.303 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2751 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 311 ; 0.279 ; 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): 60 ; 0.239 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.251 ; 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): 2663 ; 1.636 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4103 ; 2.243 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1728 ; 3.511 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1428 ; 5.402 ; 4.500 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 3KGM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB055967. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40292 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 42.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 3.810 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 7.5, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 45.63900 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 LYS B 30 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 N VAL A 172 ND2 ASN A 173 1.40 REMARK 500 NH1 ARG A 164 ND2 ASN A 170 1.46 REMARK 500 O HOH A 294 O HOH A 468 1.56 REMARK 500 CD PRO B 254 O HOH B 357 1.58 REMARK 500 O GLY A 175 O HOH A 385 1.63 REMARK 500 O HOH A 416 O HOH A 469 1.92 REMARK 500 C GLU A 171 ND2 ASN A 173 1.97 REMARK 500 NZ LYS A 30 O VAL A 285 1.97 REMARK 500 OE1 GLU B 168 O HOH B 338 2.00 REMARK 500 O LYS B 288 O HOH B 355 2.06 REMARK 500 O HOH B 351 O HOH B 410 2.07 REMARK 500 O HOH B 334 O HOH B 405 2.09 REMARK 500 NZ LYS A 30 CG1 VAL A 285 2.11 REMARK 500 O LEU B 290 O HOH B 355 2.12 REMARK 500 O THR A 96 O HOH A 467 2.13 REMARK 500 O GLU A 171 ND2 ASN A 173 2.14 REMARK 500 O VAL A 113 O HOH A 294 2.14 REMARK 500 NZ LYS A 30 O HOH A 358 2.17 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 CG GLN A 83 O HOH A 405 1655 1.55 REMARK 500 CD1 LEU A 169 OAU BB0 B 2 2656 1.87 REMARK 500 O HOH A 405 O HOH A 462 1455 1.93 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 GLN A 82 C GLN A 83 N 0.182 REMARK 500 GLN A 83 C LYS A 86 N 0.200 REMARK 500 GLU A 89 CB GLU A 89 CG 0.134 REMARK 500 GLU A 205 CG GLU A 205 CD 0.111 REMARK 500 GLY A 236 C ALA A 237 N 0.171 REMARK 500 ALA A 237 C ALA A 238 N 0.256 REMARK 500 ILE A 250 C TRP A 251 N 0.173 REMARK 500 TRP A 251 C PRO A 252 N 0.143 REMARK 500 GLU B 38 CG GLU B 38 CD 0.147 REMARK 500 TYR B 60 CD1 TYR B 60 CE1 0.104 REMARK 500 GLN B 83 C LYS B 86 N 0.190 REMARK 500 GLU B 158 CB GLU B 158 CG 0.208 REMARK 500 GLU B 230 CG GLU B 230 CD 0.095 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 GLN A 82 CA - C - N ANGL. DEV. = -13.4 DEGREES REMARK 500 GLN A 82 O - C - N ANGL. DEV. = 11.6 DEGREES REMARK 500 GLN A 83 C - N - CA ANGL. DEV. = -17.2 DEGREES REMARK 500 GLN A 83 CA - C - N ANGL. DEV. = -14.5 DEGREES REMARK 500 GLN A 83 O - C - N ANGL. DEV. = -18.0 DEGREES REMARK 500 LYS A 86 CA - C - N ANGL. DEV. = -14.6 DEGREES REMARK 500 LYS A 86 O - C - N ANGL. DEV. = 13.9 DEGREES REMARK 500 LEU A 195 CB - CG - CD1 ANGL. DEV. = 13.3 DEGREES REMARK 500 ALA A 237 O - C - N ANGL. DEV. = -18.7 DEGREES REMARK 500 ALA A 238 C - N - CA ANGL. DEV. = -15.5 DEGREES REMARK 500 ALA A 238 CA - C - N ANGL. DEV. = -15.1 DEGREES REMARK 500 ALA A 238 O - C - N ANGL. DEV. = -13.7 DEGREES REMARK 500 SER A 240 C - N - CA ANGL. DEV. = 16.3 DEGREES REMARK 500 SER A 240 CA - C - N ANGL. DEV. = -14.0 DEGREES REMARK 500 SER A 240 O - C - N ANGL. DEV. = 12.5 DEGREES REMARK 500 TRP A 251 O - C - N ANGL. DEV. = -17.4 DEGREES REMARK 500 PRO A 252 CA - C - N ANGL. DEV. = -23.4 DEGREES REMARK 500 ALA B 59 O - C - N ANGL. DEV. = -10.8 DEGREES REMARK 500 GLN B 83 O - C - N ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG B 128 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 LEU B 139 CB - CG - CD1 ANGL. DEV. = -10.2 DEGREES REMARK 500 ASP B 233 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 PRO B 252 C - N - CA ANGL. DEV. = 10.0 DEGREES REMARK 500 PRO B 252 C - N - CD ANGL. DEV. = -12.8 DEGREES REMARK 500 PRO B 254 C - N - CD ANGL. DEV. = -22.8 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 THR A 53 -13.95 -149.74 REMARK 500 ALA A 69 -145.18 58.50 REMARK 500 VAL A 103 -135.26 -121.13 REMARK 500 ASN A 106 53.93 -140.05 REMARK 500 HIS A 112 23.17 -143.23 REMARK 500 GLU A 168 -20.33 169.70 REMARK 500 VAL A 172 -44.19 -131.33 REMARK 500 ASN A 173 -113.22 -114.69 REMARK 500 GLU A 196 -130.61 -99.64 REMARK 500 LEU A 220 -125.85 -108.40 REMARK 500 ALA A 238 -161.17 -110.75 REMARK 500 PRO A 252 177.10 -51.75 REMARK 500 ARG B 61 50.63 38.20 REMARK 500 ALA B 69 -145.09 52.24 REMARK 500 VAL B 103 -137.56 -118.61 REMARK 500 GLU B 163 -47.94 -135.67 REMARK 500 GLU B 168 -58.54 171.62 REMARK 500 LEU B 169 -83.93 -154.64 REMARK 500 ASN B 170 44.23 84.07 REMARK 500 ASN B 173 -46.43 -154.81 REMARK 500 PRO B 174 -143.20 -80.50 REMARK 500 GLU B 196 -137.27 -96.13 REMARK 500 LEU B 220 -129.13 -109.97 REMARK 500 SER B 240 169.09 -31.43 REMARK 500 PRO B 254 -90.20 -0.95 REMARK 500 ALA B 272 142.46 -35.32 REMARK 500 LEU B 290 -104.73 -86.74 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 LYS A 30 ASP A 31 147.28 REMARK 500 CYS A 166 PRO A 167 -144.68 REMARK 500 PRO A 167 GLU A 168 -46.18 REMARK 500 LEU A 169 ASN A 170 -143.24 REMARK 500 ASN A 170 GLU A 171 -76.82 REMARK 500 GLU A 171 VAL A 172 -44.69 REMARK 500 ASN A 173 PRO A 174 135.77 REMARK 500 PRO A 174 GLY A 175 -40.28 REMARK 500 ALA A 237 ALA A 238 141.74 REMARK 500 PRO A 254 LYS A 255 149.69 REMARK 500 GLY A 256 ASP A 257 -148.17 REMARK 500 GLU B 168 LEU B 169 -60.95 REMARK 500 VAL B 172 ASN B 173 -30.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN A 83 28.13 REMARK 500 ALA A 237 19.47 REMARK 500 ALA A 238 26.51 REMARK 500 TRP A 251 14.76 REMARK 500 PRO A 252 27.07 REMARK 500 ALA B 238 14.97 REMARK 500 TRP B 251 -11.72 REMARK 500 PRO B 252 17.33 REMARK 500 PRO B 254 11.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 VAL A 113 24.6 L L OUTSIDE RANGE REMARK 500 VAL A 159 22.9 L L OUTSIDE RANGE REMARK 500 ASN A 170 23.1 L L OUTSIDE RANGE REMARK 500 ASN A 173 24.0 L L OUTSIDE RANGE REMARK 500 VAL A 260 23.6 L L OUTSIDE RANGE REMARK 500 VAL B 159 24.5 L L OUTSIDE RANGE REMARK 500 GLU B 168 -23.1 L D WRONG HAND REMARK 500 ASN B 170 18.5 L L OUTSIDE RANGE REMARK 500 ASN B 173 23.9 L L OUTSIDE RANGE REMARK 500 VAL B 187 24.5 L L OUTSIDE RANGE REMARK 500 VAL B 260 22.7 L L OUTSIDE RANGE 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 BB0 A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BB0 B 2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE NUMBERS 58, 84, 85, 239, 253 ARE SIMPLY SKIPPED DBREF 3KGM A 30 291 UNP P00808 BLAC_BACLI 47 303 DBREF 3KGM B 30 291 UNP P00808 BLAC_BACLI 47 303 SEQADV 3KGM CYS A 166 UNP P00808 GLU 180 ENGINEERED SEQADV 3KGM CYS B 166 UNP P00808 GLU 180 ENGINEERED SEQRES 1 A 257 LYS ASP ASP PHE ALA LYS LEU GLU GLU GLN PHE ASP ALA SEQRES 2 A 257 LYS LEU GLY ILE PHE ALA LEU ASP THR GLY THR ASN ARG SEQRES 3 A 257 THR VAL ALA TYR ARG PRO ASP GLU ARG PHE ALA PHE ALA SEQRES 4 A 257 SER THR ILE LYS ALA LEU THR VAL GLY VAL LEU LEU GLN SEQRES 5 A 257 GLN LYS SER ILE GLU ASP LEU ASN GLN ARG ILE THR TYR SEQRES 6 A 257 THR ARG ASP ASP LEU VAL ASN TYR ASN PRO ILE THR GLU SEQRES 7 A 257 LYS HIS VAL ASP THR GLY MET THR LEU LYS GLU LEU ALA SEQRES 8 A 257 ASP ALA SER LEU ARG TYR SER ASP ASN ALA ALA GLN ASN SEQRES 9 A 257 LEU ILE LEU LYS GLN ILE GLY GLY PRO GLU SER LEU LYS SEQRES 10 A 257 LYS GLU LEU ARG LYS ILE GLY ASP GLU VAL THR ASN PRO SEQRES 11 A 257 GLU ARG PHE CYS PRO GLU LEU ASN GLU VAL ASN PRO GLY SEQRES 12 A 257 GLU THR GLN ASP THR SER THR ALA ARG ALA LEU VAL THR SEQRES 13 A 257 SER LEU ARG ALA PHE ALA LEU GLU ASP LYS LEU PRO SER SEQRES 14 A 257 GLU LYS ARG GLU LEU LEU ILE ASP TRP MET LYS ARG ASN SEQRES 15 A 257 THR THR GLY ASP ALA LEU ILE ARG ALA GLY VAL PRO ASP SEQRES 16 A 257 GLY TRP GLU VAL ALA ASP LYS THR GLY ALA ALA SER TYR SEQRES 17 A 257 GLY THR ARG ASN ASP ILE ALA ILE ILE TRP PRO PRO LYS SEQRES 18 A 257 GLY ASP PRO VAL VAL LEU ALA VAL LEU SER SER ARG ASP SEQRES 19 A 257 LYS LYS ASP ALA LYS TYR ASP ASP LYS LEU ILE ALA GLU SEQRES 20 A 257 ALA THR LYS VAL VAL MET LYS ALA LEU ASN SEQRES 1 B 257 LYS ASP ASP PHE ALA LYS LEU GLU GLU GLN PHE ASP ALA SEQRES 2 B 257 LYS LEU GLY ILE PHE ALA LEU ASP THR GLY THR ASN ARG SEQRES 3 B 257 THR VAL ALA TYR ARG PRO ASP GLU ARG PHE ALA PHE ALA SEQRES 4 B 257 SER THR ILE LYS ALA LEU THR VAL GLY VAL LEU LEU GLN SEQRES 5 B 257 GLN LYS SER ILE GLU ASP LEU ASN GLN ARG ILE THR TYR SEQRES 6 B 257 THR ARG ASP ASP LEU VAL ASN TYR ASN PRO ILE THR GLU SEQRES 7 B 257 LYS HIS VAL ASP THR GLY MET THR LEU LYS GLU LEU ALA SEQRES 8 B 257 ASP ALA SER LEU ARG TYR SER ASP ASN ALA ALA GLN ASN SEQRES 9 B 257 LEU ILE LEU LYS GLN ILE GLY GLY PRO GLU SER LEU LYS SEQRES 10 B 257 LYS GLU LEU ARG LYS ILE GLY ASP GLU VAL THR ASN PRO SEQRES 11 B 257 GLU ARG PHE CYS PRO GLU LEU ASN GLU VAL ASN PRO GLY SEQRES 12 B 257 GLU THR GLN ASP THR SER THR ALA ARG ALA LEU VAL THR SEQRES 13 B 257 SER LEU ARG ALA PHE ALA LEU GLU ASP LYS LEU PRO SER SEQRES 14 B 257 GLU LYS ARG GLU LEU LEU ILE ASP TRP MET LYS ARG ASN SEQRES 15 B 257 THR THR GLY ASP ALA LEU ILE ARG ALA GLY VAL PRO ASP SEQRES 16 B 257 GLY TRP GLU VAL ALA ASP LYS THR GLY ALA ALA SER TYR SEQRES 17 B 257 GLY THR ARG ASN ASP ILE ALA ILE ILE TRP PRO PRO LYS SEQRES 18 B 257 GLY ASP PRO VAL VAL LEU ALA VAL LEU SER SER ARG ASP SEQRES 19 B 257 LYS LYS ASP ALA LYS TYR ASP ASP LYS LEU ILE ALA GLU SEQRES 20 B 257 ALA THR LYS VAL VAL MET LYS ALA LEU ASN HET BB0 A 2 16 HET BB0 B 2 16 HETNAM BB0 1-[6-(DIMETHYLAMINO)NAPHTHALEN-2-YL]ETHANONE FORMUL 3 BB0 2(C14 H15 N O) FORMUL 5 HOH *351(H2 O) HELIX 1 1 LYS A 30 ASP A 41 1 12 HELIX 2 2 THR A 71 GLN A 83 1 13 HELIX 3 3 ILE A 88 ASN A 92 5 5 HELIX 4 4 THR A 98 LEU A 102 5 5 HELIX 5 5 ILE A 108 HIS A 112 5 5 HELIX 6 6 LEU A 119 SER A 130 1 12 HELIX 7 7 ASP A 131 ILE A 142 1 12 HELIX 8 8 GLY A 143 ILE A 155 1 13 HELIX 9 9 THR A 182 LEU A 195 1 14 HELIX 10 10 PRO A 200 ARG A 213 1 14 HELIX 11 11 LEU A 220 VAL A 225 5 6 HELIX 12 12 ASP A 275 ASN A 291 1 17 HELIX 13 13 ASP B 31 PHE B 40 1 10 HELIX 14 14 THR B 71 LYS B 86 1 14 HELIX 15 15 SER B 87 ASN B 92 1 6 HELIX 16 16 THR B 98 LEU B 102 5 5 HELIX 17 17 ILE B 108 VAL B 113 5 6 HELIX 18 18 LEU B 119 SER B 130 1 12 HELIX 19 19 ASP B 131 GLY B 143 1 13 HELIX 20 20 GLY B 144 ILE B 155 1 12 HELIX 21 21 ALA B 183 LEU B 195 1 13 HELIX 22 22 PRO B 200 ARG B 213 1 14 HELIX 23 23 LEU B 220 VAL B 225 5 6 HELIX 24 24 ASP B 275 LEU B 290 1 16 SHEET 1 A 5 THR A 56 TYR A 60 0 SHEET 2 A 5 LYS A 43 ASP A 50 -1 N ILE A 46 O TYR A 60 SHEET 3 A 5 VAL A 259 SER A 266 -1 O ALA A 262 N PHE A 47 SHEET 4 A 5 ARG A 244 TRP A 251 -1 N ILE A 250 O VAL A 259 SHEET 5 A 5 GLU A 230 ALA A 237 -1 N GLU A 230 O TRP A 251 SHEET 1 B 2 PHE A 66 ALA A 67 0 SHEET 2 B 2 THR A 180 SER A 181 -1 O SER A 181 N PHE A 66 SHEET 1 C 2 ARG A 94 ILE A 95 0 SHEET 2 C 2 MET A 117 THR A 118 -1 O MET A 117 N ILE A 95 SHEET 1 D 5 THR B 56 TYR B 60 0 SHEET 2 D 5 LYS B 43 ASP B 50 -1 N ILE B 46 O TYR B 60 SHEET 3 D 5 VAL B 259 SER B 266 -1 O SER B 266 N LYS B 43 SHEET 4 D 5 THR B 243 TRP B 251 -1 N ILE B 250 O VAL B 259 SHEET 5 D 5 GLU B 230 ALA B 238 -1 N GLY B 236 O ASN B 245 SHEET 1 E 2 ARG B 65 ALA B 67 0 SHEET 2 E 2 THR B 180 THR B 182 -1 O SER B 181 N PHE B 66 SHEET 1 F 2 ARG B 94 ILE B 95 0 SHEET 2 F 2 MET B 117 THR B 118 -1 O MET B 117 N ILE B 95 LINK SG CYS A 166 CAS BB0 A 2 1555 1555 1.96 LINK SG CYS B 166 CAS BB0 B 2 1555 1555 1.87 CISPEP 1 VAL A 172 ASN A 173 0 -3.80 CISPEP 2 LEU B 169 ASN B 170 0 7.09 CISPEP 3 ASN B 173 PRO B 174 0 -14.64 SITE 1 AC1 7 VAL A 103 ASN A 104 CYS A 166 GLU A 168 SITE 2 AC1 7 ALA A 237 ALA A 238 HOH A 460 SITE 1 AC2 5 ASN B 104 ASN B 132 CYS B 166 LEU B 169 SITE 2 AC2 5 HOH B 397 CRYST1 43.812 91.278 66.472 90.00 104.81 90.00 P 1 21 1 4 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 0.022825 0.000000 0.006035 0.00000 SCALE2 0.000000 0.010956 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015561 0.00000