HEADER HYDROLASE 11-NOV-00 1HD8 TITLE CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF TITLE 2 PENICILLIN-BINDING PROTEIN 5 AT 2.3 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.16.4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 CELLULAR_LOCATION: PERIPLASM; SOURCE 5 GENE: DACA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: MC1061; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBR322; SOURCE 10 EXPRESSION_SYSTEM_GENE: DACA KEYWDS PEPTIDOGLYCAN SYNTHESIS, PENICILLIN-BINDING PROTEIN, DD- KEYWDS 2 CARBOXYPEPTIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.DAVIES,S.W.WHITE,R.A.NICHOLAS REVDAT 2 24-FEB-09 1HD8 1 VERSN REVDAT 1 08-NOV-01 1HD8 0 JRNL AUTH C.DAVIES,S.W.WHITE,R.A.NICHOLAS JRNL TITL CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE JRNL TITL 2 MUTANT OF PENICILLIN-BINDING PROTEIN 5 AT 2.3-A JRNL TITL 3 RESOLUTION JRNL REF J.BIOL.CHEM. V. 276 616 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 10967102 JRNL DOI 10.1074/JBC.M004471200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.A.NICHOLAS,J.L.STROMINGER REMARK 1 TITL RELATIONS BETWEEN BETA-LACTAMASES AND REMARK 1 TITL 2 PENICILLIN-BINDING PROTEINS: BETA-LACTAMASE REMARK 1 TITL 3 ACTIVITY OF PENICILLIN-BINDING PROTEIN 5 FROM REMARK 1 TITL 4 ESCHERICHIA COLI REMARK 1 REF REV.INFECT.DIS. V. 10 733 1988 REMARK 1 REFN ISSN 0162-0886 REMARK 1 PMID 3055172 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.BROOME-SMITH,B.G.SPRATT REMARK 1 TITL AN AMINO ACID SUBSTITUTION THAT BLOCKS THE REMARK 1 TITL 2 DEACYLATION STEP IN THE ENZYME MECHANISM OF REMARK 1 TITL 3 PENICILLIN-BINDING PROTEIN 5 OF ESCHERICHIA COLI REMARK 1 REF FEBS LETT. V. 165 185 1984 REMARK 1 REFN ISSN 0014-5793 REMARK 1 PMID 6319180 REMARK 1 DOI 10.1016/0014-5793(84)80166-0 REMARK 2 REMARK 2 RESOLUTION. 2.3 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.3 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.0 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 17184 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.0 REMARK 3 FREE R VALUE TEST SET COUNT : 1693 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2606 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.372 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.284 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.210 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.60 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.013 ; 0.02 REMARK 3 ANGLE DISTANCE (A) : 0.043 ; 0.04 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.074 ; 0.05 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.0244; 0.03 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.148 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.191 ; 0.30 REMARK 3 MULTIPLE TORSION (A) : 0.257 ; 0.30 REMARK 3 H-BOND (X...Y) (A) : 0.187 ; 0.30 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 9.8 ; 7.0 REMARK 3 STAGGERED (DEGREES) : 19.9 ; 15.0 REMARK 3 TRANSVERSE (DEGREES) : 22.8 ; 20.0 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.642 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.541 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.864 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.920 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: XPLOR USED IN EARLY STAGES OF REMARK 3 REFINEMENT REMARK 4 REMARK 4 1HD8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-NOV-00. REMARK 100 THE PDBE ID CODE IS EBI-5294. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.00 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 : NONIUS FR391 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17239 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 22.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 2.520 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29400 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.5 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% POLYETHYLENE GLYCOL 4000, REMARK 280 50 MM TRIS PH 7.0, 0.2 % SODIUM AZIDE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.52667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.76333 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 GENERATING THE BIOMOLECULE 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: PQS 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 400 REMARK 400 COMPOUND REMARK 400 CHAIN A ENGINEERED MUTATION GLY105ASP REMARK 400 TO PRODUCE SPBP 5', THE LAST 17 AMINO ACIDS WERE REMARK 400 REMOVED BY DELETION OF THEIR RESPECTIVE CODONS, BUT REMARK 400 AN ADDITIONAL SIX AMINO ACIDS (GDPVID) WERE INTRODUCED REMARK 400 AT THE C TERMINUS DUE TO READ-THROUGH TO THE STOP REMARK 400 CODON. NONE OF THESE NON-NATIVE RESIDUES ARE VISIBLE REMARK 400 IN THE ELECTRON DENSITY MAP. REMARK 400 THE FIRST 29 AMINO ACIDS OF THE PROTEIN ENCODED BY REMARK 400 THE OPEN READING FRAME REPRESENT THE SIGNAL SEQUENCE, REMARK 400 WHICH IS REMOVED DURING MATURATION AND TRANSPORT TO REMARK 400 THE PERIPLASMIC SPACE AND IS NOT PRESENT IN THIS REMARK 400 CONSTRUCT. 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 ASP A 1 REMARK 465 ASP A 2 REMARK 465 ASP A 74 REMARK 465 ALA A 75 REMARK 465 TRP A 76 REMARK 465 ALA A 77 REMARK 465 THR A 78 REMARK 465 GLY A 79 REMARK 465 ASN A 80 REMARK 465 PRO A 81 REMARK 465 VAL A 82 REMARK 465 PHE A 83 REMARK 465 LYS A 84 REMARK 465 GLY A 85 REMARK 465 SER A 86 REMARK 465 SER A 87 REMARK 465 LEU A 88 REMARK 465 MET A 89 REMARK 465 PHE A 90 REMARK 465 PHE A 357 REMARK 465 GLY A 358 REMARK 465 ASP A 359 REMARK 465 PRO A 360 REMARK 465 VAL A 361 REMARK 465 ILE A 362 REMARK 465 ASP A 363 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 GLY A 157 N GLY A 157 CA -0.106 REMARK 500 ILE A 212 N ILE A 212 CA -0.121 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 3 CB - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 LEU A 3 CA - C - O ANGL. DEV. = 28.4 DEGREES REMARK 500 ASN A 4 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 LEU A 3 CA - C - N ANGL. DEV. = -18.0 DEGREES REMARK 500 LEU A 3 O - C - N ANGL. DEV. = -11.6 DEGREES REMARK 500 ASN A 4 C - N - CA ANGL. DEV. = 32.7 DEGREES REMARK 500 ARG A 39 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = -10.3 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = 14.0 DEGREES REMARK 500 ASP A 105 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 GLN A 126 CG - CD - OE1 ANGL. DEV. = 12.4 DEGREES REMARK 500 ASP A 154 CA - C - O ANGL. DEV. = 13.4 DEGREES REMARK 500 ASP A 154 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 154 CA - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 ASP A 156 CA - CB - CG ANGL. DEV. = -15.1 DEGREES REMARK 500 ASP A 156 CA - C - O ANGL. DEV. = 22.5 DEGREES REMARK 500 GLY A 157 CA - C - O ANGL. DEV. = 13.0 DEGREES REMARK 500 GLY A 157 N - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 ASP A 156 O - C - N ANGL. DEV. = -13.5 DEGREES REMARK 500 GLY A 157 C - N - CA ANGL. DEV. = 37.1 DEGREES REMARK 500 ARG A 174 CD - NE - CZ ANGL. DEV. = 46.8 DEGREES REMARK 500 ARG A 174 CG - CD - NE ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG A 174 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP A 175 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TYR A 183 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES REMARK 500 TYR A 183 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 204 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 210 CB - CG - OD1 ANGL. DEV. = 8.3 DEGREES REMARK 500 GLY A 211 CA - C - O ANGL. DEV. = 11.1 DEGREES REMARK 500 ILE A 212 C - N - CA ANGL. DEV. = 57.0 DEGREES REMARK 500 ARG A 234 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG A 234 NE - CZ - NH1 ANGL. DEV. = -11.7 DEGREES REMARK 500 ARG A 234 NE - CZ - NH2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG A 243 NE - CZ - NH1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 248 CD - NE - CZ ANGL. DEV. = 11.3 DEGREES REMARK 500 ARG A 248 CG - CD - NE ANGL. DEV. = 16.6 DEGREES REMARK 500 ARG A 248 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 261 NE - CZ - NH2 ANGL. DEV. = 7.1 DEGREES REMARK 500 PHE A 262 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP A 284 CA - CB - CG ANGL. DEV. = 17.2 DEGREES REMARK 500 SER A 285 N - CA - CB ANGL. DEV. = 12.4 DEGREES REMARK 500 ARG A 287 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 VAL A 292 N - CA - CB ANGL. DEV. = -13.6 DEGREES REMARK 500 ARG A 304 CG - CD - NE ANGL. DEV. = 15.1 DEGREES REMARK 500 ALA A 321 CA - C - O ANGL. DEV. = -19.2 DEGREES REMARK 500 ALA A 321 O - C - N ANGL. DEV. = 13.6 DEGREES REMARK 500 PRO A 322 C - N - CA ANGL. DEV. = 13.6 DEGREES REMARK 500 ARG A 344 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 344 NE - CZ - NH2 ANGL. DEV. = -3.4 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 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 ASN A 4 -37.12 -11.09 REMARK 500 ALA A 43 -125.74 57.60 REMARK 500 GLN A 148 -30.37 -131.41 REMARK 500 ASN A 208 78.22 -110.42 REMARK 500 ILE A 212 -110.29 131.19 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 GLY A 211 ILE A 212 109.66 REMARK 500 ALA A 321 PRO A 322 -32.14 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, 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 SER A 27 11.39 REMARK 500 LEU A 153 12.15 REMARK 500 TYR A 180 -12.38 REMARK 500 ASN A 315 10.20 REMARK 500 ALA A 321 -14.57 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 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 ILE A 212 16.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): DBREF 1HD8 A 1 357 UNP P04287 DACA_ECOLI 30 386 DBREF 1HD8 A 358 363 PDB 1HD8 1HD8 358 363 SEQADV 1HD8 ASP A 105 UNP P04287 GLY 105 ENGINEERED MUTATION SEQRES 1 A 363 ASP ASP LEU ASN ILE LYS THR MET ILE PRO GLY VAL PRO SEQRES 2 A 363 GLN ILE ASP ALA GLU SER TYR ILE LEU ILE ASP TYR ASN SEQRES 3 A 363 SER GLY LYS VAL LEU ALA GLU GLN ASN ALA ASP VAL ARG SEQRES 4 A 363 ARG ASP PRO ALA SER LEU THR LYS MET MET THR SER TYR SEQRES 5 A 363 VAL ILE GLY GLN ALA MET LYS ALA GLY LYS PHE LYS GLU SEQRES 6 A 363 THR ASP LEU VAL THR ILE GLY ASN ASP ALA TRP ALA THR SEQRES 7 A 363 GLY ASN PRO VAL PHE LYS GLY SER SER LEU MET PHE LEU SEQRES 8 A 363 LYS PRO GLY MET GLN VAL PRO VAL SER GLN LEU ILE ARG SEQRES 9 A 363 ASP ILE ASN LEU GLN SER GLY ASN ASP ALA CYS VAL ALA SEQRES 10 A 363 MET ALA ASP PHE ALA ALA GLY SER GLN ASP ALA PHE VAL SEQRES 11 A 363 GLY LEU MET ASN SER TYR VAL ASN ALA LEU GLY LEU LYS SEQRES 12 A 363 ASN THR HIS PHE GLN THR VAL HIS GLY LEU ASP ALA ASP SEQRES 13 A 363 GLY GLN TYR SER SER ALA ARG ASP MET ALA LEU ILE GLY SEQRES 14 A 363 GLN ALA LEU ILE ARG ASP VAL PRO ASN GLU TYR SER ILE SEQRES 15 A 363 TYR LYS GLU LYS GLU PHE THR PHE ASN GLY ILE ARG GLN SEQRES 16 A 363 LEU ASN ARG ASN GLY LEU LEU TRP ASP ASN SER LEU ASN SEQRES 17 A 363 VAL ASP GLY ILE LYS THR GLY HIS THR ASP LYS ALA GLY SEQRES 18 A 363 TYR ASN LEU VAL ALA SER ALA THR GLU GLY GLN MET ARG SEQRES 19 A 363 LEU ILE SER ALA VAL MET GLY GLY ARG THR PHE LYS GLY SEQRES 20 A 363 ARG GLU ALA GLU SER LYS LYS LEU LEU THR TRP GLY PHE SEQRES 21 A 363 ARG PHE PHE GLU THR VAL ASN PRO LEU LYS VAL GLY LYS SEQRES 22 A 363 GLU PHE ALA SER GLU PRO VAL TRP PHE GLY ASP SER ASP SEQRES 23 A 363 ARG ALA SER LEU GLY VAL ASP LYS ASP VAL TYR LEU THR SEQRES 24 A 363 ILE PRO ARG GLY ARG MET LYS ASP LEU LYS ALA SER TYR SEQRES 25 A 363 VAL LEU ASN SER SER GLU LEU HIS ALA PRO LEU GLN LYS SEQRES 26 A 363 ASN GLN VAL VAL GLY THR ILE ASN PHE GLN LEU ASP GLY SEQRES 27 A 363 LYS THR ILE GLU GLN ARG PRO LEU VAL VAL LEU GLN GLU SEQRES 28 A 363 ILE PRO GLU GLY ASN PHE GLY ASP PRO VAL ILE ASP FORMUL 2 HOH *145(H2 O1) HELIX 1 1 PRO A 42 LEU A 45 5 4 HELIX 2 2 THR A 46 ALA A 60 1 15 HELIX 3 3 VAL A 99 SER A 110 1 12 HELIX 4 4 GLY A 111 GLY A 124 1 14 HELIX 5 5 SER A 125 GLY A 141 1 17 HELIX 6 6 SER A 161 VAL A 176 1 16 HELIX 7 7 VAL A 176 SER A 181 1 6 HELIX 8 8 ILE A 182 GLU A 185 5 4 HELIX 9 9 ASN A 199 ASP A 204 5 6 HELIX 10 10 LYS A 246 PHE A 262 1 17 HELIX 11 11 ARG A 304 LEU A 308 5 5 SHEET 1 AA 5 VAL A 30 GLN A 34 0 SHEET 2 AA 5 ALA A 17 ASP A 24 -1 O TYR A 20 N GLN A 34 SHEET 3 AA 5 MET A 233 GLY A 242 -1 O ILE A 236 N ILE A 23 SHEET 4 AA 5 GLY A 221 GLU A 230 -1 O TYR A 222 N GLY A 242 SHEET 5 AA 5 VAL A 209 THR A 217 -1 N ASP A 210 O SER A 227 SHEET 1 AB 2 LEU A 68 THR A 70 0 SHEET 2 AB 2 GLN A 96 PRO A 98 -1 O VAL A 97 N VAL A 69 SHEET 1 AC 2 GLU A 187 PHE A 190 0 SHEET 2 AC 2 ILE A 193 LEU A 196 -1 O ILE A 193 N PHE A 190 SHEET 1 AD 2 PHE A 263 LEU A 269 0 SHEET 2 AD 2 VAL A 296 PRO A 301 -1 O VAL A 296 N LEU A 269 SHEET 1 AE 6 LYS A 309 LEU A 314 0 SHEET 2 AE 6 VAL A 328 LEU A 336 -1 O THR A 331 N VAL A 313 SHEET 3 AE 6 LYS A 339 VAL A 348 -1 O LYS A 339 N LEU A 336 SHEET 4 AE 6 ARG A 287 GLY A 291 -1 O GLY A 291 N VAL A 347 SHEET 5 AE 6 ALA A 276 TRP A 281 -1 O ALA A 276 N LEU A 290 SHEET 6 AE 6 LEU A 319 HIS A 320 1 O LEU A 319 N TRP A 281 CRYST1 50.830 50.830 140.290 90.00 90.00 120.00 P 32 3 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 0.019673 0.011358 0.000000 0.00000 SCALE2 0.000000 0.022717 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007128 0.00000