HEADER ISOMERASE 29-SEP-98 1BWZ TITLE DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (DIAMINOPIMELATE EPIMERASE); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DAP EPIMERASE; COMPND 5 EC: 5.1.1.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 GENE: DAPF; 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_PLASMID: PET 23A(+); SOURCE 9 EXPRESSION_SYSTEM_GENE: DAPF KEYWDS METABOLIC ROLE, STRUCTURAL CLASSIFICATION, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.CIRILLI,R.ZHENG,G.SCAPIN,J.S.BLANCHARD REVDAT 4 04-OCT-17 1BWZ 1 REMARK REVDAT 3 24-FEB-09 1BWZ 1 VERSN REVDAT 2 29-DEC-99 1BWZ 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 16-DEC-98 1BWZ 0 JRNL AUTH M.CIRILLI,R.ZHENG,G.SCAPIN,J.S.BLANCHARD JRNL TITL STRUCTURAL SYMMETRY: THE THREE-DIMENSIONAL STRUCTURE OF JRNL TITL 2 HAEMOPHILUS INFLUENZAE DIAMINOPIMELATE EPIMERASE. JRNL REF BIOCHEMISTRY V. 37 16452 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9843410 JRNL DOI 10.1021/BI982138O REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.8 REMARK 3 NUMBER OF REFLECTIONS : 9411 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 SET) : 0.190 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2117 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.65 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.825 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.59 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARAM19X.PR REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008247. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 288 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9691 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 23.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 11.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.06100 REMARK 200 FOR SHELL : 10.89 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 33.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.05000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.70000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.05000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.70000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.15000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.05000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.70000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 33.15000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.05000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.70000 REMARK 290 SMTRY3 8 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 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 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 THR A 273 OG1 CG2 REMARK 470 LEU A 274 CG CD1 CD2 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 ASN A 22 44.67 -86.87 REMARK 500 PHE A 24 115.76 -166.50 REMARK 500 ASP A 53 114.44 -167.34 REMARK 500 SER A 71 72.09 -172.37 REMARK 500 GLN A 146 157.72 175.82 REMARK 500 ASN A 171 63.67 -67.60 REMARK 500 SER A 181 61.92 -106.62 REMARK 500 ARG A 188 -174.34 60.93 REMARK 500 ALA A 211 -47.73 -132.29 REMARK 500 ASN A 237 89.25 68.63 REMARK 500 ILE A 267 -60.20 -94.79 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BWZ A 1 274 UNP P44859 DAPF_HAEIN 1 274 SEQADV 1BWZ MET A 111 UNP P44859 ASP 111 CONFLICT SEQRES 1 A 274 MET GLN PHE SER LYS MET HIS GLY LEU GLY ASN ASP PHE SEQRES 2 A 274 VAL VAL VAL ASP GLY VAL THR GLN ASN VAL PHE PHE THR SEQRES 3 A 274 PRO GLU THR ILE ARG ARG LEU ALA ASN ARG HIS CYS GLY SEQRES 4 A 274 ILE GLY PHE ASP GLN LEU LEU ILE VAL GLU ALA PRO TYR SEQRES 5 A 274 ASP PRO GLU LEU ASP PHE HIS TYR ARG ILE PHE ASN ALA SEQRES 6 A 274 ASP GLY SER GLU VAL SER GLN CYS GLY ASN GLY ALA ARG SEQRES 7 A 274 CYS PHE ALA ARG PHE VAL THR LEU LYS GLY LEU THR ASN SEQRES 8 A 274 LYS LYS ASP ILE SER VAL SER THR GLN LYS GLY ASN MET SEQRES 9 A 274 VAL LEU THR VAL LYS ASP MET ASN GLN ILE ARG VAL ASN SEQRES 10 A 274 MET GLY GLU PRO ILE TRP GLU PRO ALA LYS ILE PRO PHE SEQRES 11 A 274 THR ALA ASN LYS PHE GLU LYS ASN TYR ILE LEU ARG THR SEQRES 12 A 274 ASP ILE GLN THR VAL LEU CYS GLY ALA VAL SER MET GLY SEQRES 13 A 274 ASN PRO HIS CYS VAL VAL GLN VAL ASP ASP ILE GLN THR SEQRES 14 A 274 ALA ASN VAL GLU GLN LEU GLY PRO LEU LEU GLU SER HIS SEQRES 15 A 274 GLU ARG PHE PRO GLU ARG VAL ASN ALA GLY PHE MET GLN SEQRES 16 A 274 ILE ILE ASN LYS GLU HIS ILE LYS LEU ARG VAL TYR GLU SEQRES 17 A 274 ARG GLY ALA GLY GLU THR GLN ALA CYS GLY SER GLY ALA SEQRES 18 A 274 CYS ALA ALA VAL ALA VAL GLY ILE MET GLN GLY LEU LEU SEQRES 19 A 274 ASN ASN ASN VAL GLN VAL ASP LEU PRO GLY GLY SER LEU SEQRES 20 A 274 MET ILE GLU TRP ASN GLY VAL GLY HIS PRO LEU TYR MET SEQRES 21 A 274 THR GLY GLU ALA THR HIS ILE TYR ASP GLY PHE ILE THR SEQRES 22 A 274 LEU FORMUL 2 HOH *29(H2 O) HELIX 1 1 PRO A 27 ALA A 34 1 8 HELIX 2 2 ALA A 77 LEU A 86 1 10 HELIX 3 3 PRO A 125 LYS A 127 5 3 HELIX 4 4 VAL A 172 GLU A 180 1 9 HELIX 5 5 GLY A 218 MET A 230 1 13 SHEET 1 A 5 HIS A 59 ASN A 64 0 SHEET 2 A 5 GLN A 44 GLU A 49 -1 N GLU A 49 O HIS A 59 SHEET 3 A 5 ASN A 11 ASP A 17 1 N VAL A 14 O GLN A 44 SHEET 4 A 5 GLN A 2 GLY A 8 -1 N GLY A 8 O ASN A 11 SHEET 5 A 5 THR A 265 PHE A 271 -1 N GLY A 270 O PHE A 3 SHEET 1 B10 ASP A 94 SER A 98 0 SHEET 2 B10 ASN A 103 VAL A 108 -1 N LEU A 106 O ILE A 95 SHEET 3 B10 ILE A 114 ASN A 117 -1 N ASN A 117 O VAL A 105 SHEET 4 B10 TYR A 259 GLY A 262 -1 N GLY A 262 O ILE A 114 SHEET 5 B10 SER A 246 GLU A 250 -1 N GLU A 250 O TYR A 259 SHEET 6 B10 VAL A 238 ASP A 241 -1 N VAL A 240 O LEU A 247 SHEET 7 B10 HIS A 201 TYR A 207 1 N ILE A 202 O GLN A 239 SHEET 8 B10 ASN A 190 ASN A 198 -1 N ASN A 198 O HIS A 201 SHEET 9 B10 PRO A 158 GLN A 163 1 N CYS A 160 O ASN A 190 SHEET 10 B10 GLY A 151 SER A 154 -1 N VAL A 153 O HIS A 159 SHEET 1 C 2 TYR A 139 THR A 143 0 SHEET 2 C 2 GLN A 146 CYS A 150 -1 N CYS A 150 O TYR A 139 SSBOND 1 CYS A 73 CYS A 217 1555 1555 2.03 CISPEP 1 ILE A 128 PRO A 129 0 -0.41 CRYST1 102.100 115.400 66.300 90.00 90.00 90.00 C 2 2 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 0.009794 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008665 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015083 0.00000