10 20 30 40 50 60 70 80 1B0A - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE,HYDROLASE 06-NOV-98 1B0A
TITLE 5,10, METHYLENE-TETRAHYDROPHOLATE TITLE 2 DEHYDROGENASE/CYCLOHYDROLASE FROM E COLI.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (FOLD BIFUNCTIONAL PROTEIN); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: BL21; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B
KEYWDS FOLATE, DEHYDROGENASE, CYCLCOHYDROLASE, BIFUNCTIONAL, KEYWDS 2 CHANNELING, OXIDOREDUCTASE,HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR B.W.SHEN,D.DYER,J.-Y.HUANG,L.D'ARI,J.RABINOWITZ,B.L.STODDARD
REVDAT 3 24-FEB-09 1B0A 1 VERSN REVDAT 2 01-APR-03 1B0A 1 JRNL REVDAT 1 29-JUN-99 1B0A 0
JRNL AUTH B.W.SHEN,D.H.DYER,J.Y.HUANG,L.D'ARI,J.RABINOWITZ, JRNL AUTH 2 B.L.STODDARD JRNL TITL THE CRYSTAL STRUCTURE OF A BACTERIAL, BIFUNCTIONAL JRNL TITL 2 5,10 METHYLENE-TETRAHYDROFOLATE JRNL TITL 3 DEHYDROGENASE/CYCLOHYDROLASE. JRNL REF PROTEIN SCI. V. 8 1342 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10386884
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 12723 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.68 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1354 REMARK 3 BIN R VALUE (WORKING SET) : 0.3760 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.36 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 154 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 : 2173 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.40 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.20 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULKSOLVENT CORRECTION
REMARK 4 REMARK 4 1B0A COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-98. REMARK 100 THE RCSB ID CODE IS RCSB000030.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 170.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12965 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.13000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 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 (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 32.26000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.47500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 73.07000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.26000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.47500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.07000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.26000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.47500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.07000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.26000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 42.47500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.07000 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: DIMERIC 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 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 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 MET A 1
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 ASP A 7 85.14 -66.03 REMARK 500 ARG A 134 19.90 51.83 REMARK 500 ARG A 137 -114.43 -111.91 REMARK 500 VAL A 171 -71.24 -129.05 REMARK 500 HIS A 190 -146.39 -155.52 REMARK 500 ALA A 209 58.30 -148.67 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): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 305 DISTANCE = 5.33 ANGSTROMS REMARK 525 HOH A 322 DISTANCE = 5.67 ANGSTROMS REMARK 525 HOH A 323 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH A 327 DISTANCE = 5.12 ANGSTROMS REMARK 525 HOH A 352 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A 355 DISTANCE = 5.63 ANGSTROMS
DBREF 1B0A A 1 288 UNP P24186 FOLD_ECOLI 1 288
SEQRES 1 A 288 MET ALA ALA LYS ILE ILE ASP GLY LYS THR ILE ALA GLN SEQRES 2 A 288 GLN VAL ARG SER GLU VAL ALA GLN LYS VAL GLN ALA ARG SEQRES 3 A 288 ILE ALA ALA GLY LEU ARG ALA PRO GLY LEU ALA VAL VAL SEQRES 4 A 288 LEU VAL GLY SER ASN PRO ALA SER GLN ILE TYR VAL ALA SEQRES 5 A 288 SER LYS ARG LYS ALA CYS GLU GLU VAL GLY PHE VAL SER SEQRES 6 A 288 ARG SER TYR ASP LEU PRO GLU THR THR SER GLU ALA GLU SEQRES 7 A 288 LEU LEU GLU LEU ILE ASP THR LEU ASN ALA ASP ASN THR SEQRES 8 A 288 ILE ASP GLY ILE LEU VAL GLN LEU PRO LEU PRO ALA GLY SEQRES 9 A 288 ILE ASP ASN VAL LYS VAL LEU GLU ARG ILE HIS PRO ASP SEQRES 10 A 288 LYS ASP VAL ASP GLY PHE HIS PRO TYR ASN VAL GLY ARG SEQRES 11 A 288 LEU CYS GLN ARG ALA PRO ARG LEU ARG PRO CYS THR PRO SEQRES 12 A 288 ARG GLY ILE VAL THR LEU LEU GLU ARG TYR ASN ILE ASP SEQRES 13 A 288 THR PHE GLY LEU ASN ALA VAL VAL ILE GLY ALA SER ASN SEQRES 14 A 288 ILE VAL GLY ARG PRO MET SER MET GLU LEU LEU LEU ALA SEQRES 15 A 288 GLY CYS THR THR THR VAL THR HIS ARG PHE THR LYS ASN SEQRES 16 A 288 LEU ARG HIS HIS VAL GLU ASN ALA ASP LEU LEU ILE VAL SEQRES 17 A 288 ALA VAL GLY LYS PRO GLY PHE ILE PRO GLY ASP TRP ILE SEQRES 18 A 288 LYS GLU GLY ALA ILE VAL ILE ASP VAL GLY ILE ASN ARG SEQRES 19 A 288 LEU GLU ASN GLY LYS VAL VAL GLY ASP VAL VAL PHE GLU SEQRES 20 A 288 ASP ALA ALA LYS ARG ALA SER TYR ILE THR PRO VAL PRO SEQRES 21 A 288 GLY GLY VAL GLY PRO MET THR VAL ALA THR LEU ILE GLU SEQRES 22 A 288 ASN THR LEU GLN ALA CYS VAL GLU TYR HIS ASP PRO GLN SEQRES 23 A 288 ASP GLU
FORMUL 2 HOH *61(H2 O)
HELIX 1 H1 GLY A 8 ALA A 29 1 22 HELIX 2 H2 PRO A 45 VAL A 61 1 17 HELIX 3 H3 GLU A 76 ASP A 89 1 14 HELIX 4 H4 ASP A 106 ARG A 113 1 8 HELIX 5 H5 HIS A 124 GLN A 133 1 10 HELIX 6 H6 CYS A 141 ASN A 154 1 14 HELIX 7 H7 GLY A 172 ALA A 182 1 11 HELIX 8 H8 LEU A 196 ASN A 202 1 7 HELIX 9 H9 PRO A 217 ILE A 221 5 5 HELIX 10 H10 PHE A 246 ARG A 252 1 7 HELIX 11 H11 VAL A 259 TYR A 282 1 24
SHEET 1 S1 6 ALA A 3 ILE A 6 0 SHEET 2 S1 6 GLY A 159 GLY A 166 1 SHEET 3 S1 6 CYS A 184 HIS A 190 1 SHEET 4 S1 6 ASP A 204 ALA A 209 1 SHEET 5 S1 6 ALA A 225 VAL A 230 1 SHEET 6 S1 6 SER A 254 THR A 257 1 SHEET 1 S2 3 PRO A 34 GLY A 42 0 SHEET 2 S2 3 VAL A 64 PRO A 71 1 SHEET 3 S2 3 ASP A 93 GLN A 98 1 SHEET 1 S3 2 ILE A 232 LEU A 235 0 SHEET 2 S3 2 LYS A 239 GLY A 242 -1
CISPEP 1 LEU A 99 PRO A 100 0 0.00 CISPEP 2 VAL A 259 PRO A 260 0 -0.29
CRYST1 64.520 84.950 146.140 90.00 90.00 90.00 I 2 2 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 0.015499 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011772 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006843 0.00000