HEADER PURINE BIOSYNTHESIS 13-MAY-98 2GAR TITLE A PH-DEPENDENT STABLIZATION OF AN ACTIVE SITE LOOP OBSERVED FROM LOW TITLE 2 AND HIGH PH CRYSTAL STRUCTURES OF MUTANT MONOMERIC GLYCINAMIDE TITLE 3 RIBONUCLEOTIDE TRANSFORMYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GARTFASE; COMPND 5 EC: 2.1.2.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PURINE BIOSYNTHESIS, FOLATE COFACTORS, LOOP FLEXIBILITY, MONOMER- KEYWDS 2 DIMER ASSOCIATION, ENZYME MECHANISM, ANTI-CANCER AGENTS EXPDTA X-RAY DIFFRACTION AUTHOR Y.SU,M.M.YAMASHITA,S.E.GREASLEY,C.A.MULLEN,J.H.SHIM,P.A.JENNINGS, AUTHOR 2 S.J.BENKOVIC,I.A.WILSON REVDAT 5 29-MAY-24 2GAR 1 REMARK REVDAT 4 09-AUG-23 2GAR 1 REMARK REVDAT 3 03-NOV-21 2GAR 1 REMARK SEQADV REVDAT 2 24-FEB-09 2GAR 1 VERSN REVDAT 1 12-AUG-98 2GAR 0 JRNL AUTH Y.SU,M.M.YAMASHITA,S.E.GREASLEY,C.A.MULLEN,J.H.SHIM, JRNL AUTH 2 P.A.JENNINGS,S.J.BENKOVIC,I.A.WILSON JRNL TITL A PH-DEPENDENT STABILIZATION OF AN ACTIVE SITE LOOP OBSERVED JRNL TITL 2 FROM LOW AND HIGH PH CRYSTAL STRUCTURES OF MUTANT MONOMERIC JRNL TITL 3 GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE AT 1.8 TO 1.9 A. JRNL REF J.MOL.BIOL. V. 281 485 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9698564 JRNL DOI 10.1006/JMBI.1998.1931 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.KLEIN,P.CHEN,J.H.AREVALO,E.A.STURA,A.MAROLEWSKI, REMARK 1 AUTH 2 M.S.WARREN,S.J.BENKOVIC,I.A.WILSON REMARK 1 TITL TOWARDS STRUCTURE-BASED DRUG DESIGN: CRYSTAL STRUCTURE OF A REMARK 1 TITL 2 MULTISUBSTRATE ADDUCT COMPLEX OF GLYCINAMIDE RIBONUCLEOTIDE REMARK 1 TITL 3 TRANSFORMYLASE AT 1.96 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 249 153 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.J.ALMASSY,C.A.JANSON,C.C.KAN,Z.HOSTOMSKA REMARK 1 TITL STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE REMARK 1 TITL 2 RIBONUCLEOTIDE TRANSFORMYLASE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 89 6114 1992 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 3 REMARK 1 AUTH P.CHEN,U.SCHULZE-GAHMEN,E.A.STURA,J.INGLESE,D.L.JOHNSON, REMARK 1 AUTH 2 A.MAROLEWSKI,S.J.BENKOVIC,I.A.WILSON REMARK 1 TITL CRYSTAL STRUCTURE OF GLYCINAMIDE RIBONUCLEOTIDE REMARK 1 TITL 2 TRANSFORMYLASE FROM ESCHERICHIA COLI AT 3.0 A RESOLUTION. A REMARK 1 TITL 3 TARGET ENZYME FOR CHEMOTHERAPY REMARK 1 REF J.MOL.BIOL. V. 227 283 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 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) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 20923 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) : 0.201 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1807 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2138 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 241 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1443 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.00 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 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 : PO4.PAR REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : PO4.PRO REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 RESIDUES 111 - 131 HAVE NO OBSERVABLE ELECTRON DENSITY AND REMARK 3 ARE NOT INCLUDED IN THE FINAL MODEL. RESIDUES 141 - 145, REMARK 3 AND 158 - 165 ARE LOCATED IN FLEXIBLE LOOPS AND HAVE HIGH REMARK 3 B FACTORS. REMARK 4 REMARK 4 2GAR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178120. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAR-97 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS 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 : 21864 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : 0.28700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.8 REMARK 200 STARTING MODEL: PDB ENTRY 1GAR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTAL GREW FROM A SOLUTION OF REMARK 280 2%(V/V) 15% (W/V) PEG 1500, PH 3.5 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 22.90000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.60000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.60000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.90000 REMARK 290 SMTRY3 4 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 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 LEU A 111 REMARK 465 LEU A 112 REMARK 465 PRO A 113 REMARK 465 LYS A 114 REMARK 465 TYR A 115 REMARK 465 PRO A 116 REMARK 465 GLY A 117 REMARK 465 LEU A 118 REMARK 465 HIS A 119 REMARK 465 THR A 120 REMARK 465 HIS A 121 REMARK 465 ARG A 122 REMARK 465 GLN A 123 REMARK 465 ALA A 124 REMARK 465 LEU A 125 REMARK 465 GLU A 126 REMARK 465 ASN A 127 REMARK 465 GLY A 128 REMARK 465 ASP A 129 REMARK 465 GLU A 130 REMARK 465 GLU A 131 REMARK 465 ALA A 210 REMARK 465 ASP A 211 REMARK 465 GLU A 212 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 O HOH A 539 O HOH A 616 2.17 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 PO4 A 221 DBREF 2GAR A 1 212 UNP P08179 PUR3_ECOLI 1 212 SEQADV 2GAR ALA A 70 UNP P08179 GLU 70 ENGINEERED MUTATION SEQRES 1 A 212 MET ASN ILE VAL VAL LEU ILE SER GLY ASN GLY SER ASN SEQRES 2 A 212 LEU GLN ALA ILE ILE ASP ALA CYS LYS THR ASN LYS ILE SEQRES 3 A 212 LYS GLY THR VAL ARG ALA VAL PHE SER ASN LYS ALA ASP SEQRES 4 A 212 ALA PHE GLY LEU GLU ARG ALA ARG GLN ALA GLY ILE ALA SEQRES 5 A 212 THR HIS THR LEU ILE ALA SER ALA PHE ASP SER ARG GLU SEQRES 6 A 212 ALA TYR ASP ARG ALA LEU ILE HIS GLU ILE ASP MET TYR SEQRES 7 A 212 ALA PRO ASP VAL VAL VAL LEU ALA GLY PHE MET ARG ILE SEQRES 8 A 212 LEU SER PRO ALA PHE VAL SER HIS TYR ALA GLY ARG LEU SEQRES 9 A 212 LEU ASN ILE HIS PRO SER LEU LEU PRO LYS TYR PRO GLY SEQRES 10 A 212 LEU HIS THR HIS ARG GLN ALA LEU GLU ASN GLY ASP GLU SEQRES 11 A 212 GLU HIS GLY THR SER VAL HIS PHE VAL THR ASP GLU LEU SEQRES 12 A 212 ASP GLY GLY PRO VAL ILE LEU GLN ALA LYS VAL PRO VAL SEQRES 13 A 212 PHE ALA GLY ASP SER GLU ASP ASP ILE THR ALA ARG VAL SEQRES 14 A 212 GLN THR GLN GLU HIS ALA ILE TYR PRO LEU VAL ILE SER SEQRES 15 A 212 TRP PHE ALA ASP GLY ARG LEU LYS MET HIS GLU ASN ALA SEQRES 16 A 212 ALA TRP LEU ASP GLY GLN ARG LEU PRO PRO GLN GLY TYR SEQRES 17 A 212 ALA ALA ASP GLU HET PO4 A 221 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *124(H2 O) HELIX 1 1 SER A 12 LYS A 22 1 11 HELIX 2 2 PHE A 41 GLN A 48 1 8 HELIX 3 3 ALA A 58 ALA A 60 5 3 HELIX 4 4 ARG A 64 TYR A 78 1 15 HELIX 5 5 PRO A 94 HIS A 99 1 6 HELIX 6 6 GLU A 162 ALA A 185 1 24 SHEET 1 A 7 VAL A 148 LYS A 153 0 SHEET 2 A 7 GLY A 133 PHE A 138 -1 N VAL A 136 O ILE A 149 SHEET 3 A 7 LEU A 104 HIS A 108 -1 N HIS A 108 O SER A 135 SHEET 4 A 7 VAL A 82 LEU A 85 1 N VAL A 83 O LEU A 105 SHEET 5 A 7 ASN A 2 ILE A 7 1 N VAL A 4 O VAL A 82 SHEET 6 A 7 THR A 29 SER A 35 1 N THR A 29 O ILE A 3 SHEET 7 A 7 ALA A 52 THR A 55 1 N ALA A 52 O VAL A 33 SHEET 1 B 2 LEU A 189 HIS A 192 0 SHEET 2 B 2 ALA A 195 LEU A 198 -1 N TRP A 197 O LYS A 190 SITE 1 AC1 8 ASN A 10 GLY A 11 SER A 12 ASN A 13 SITE 2 AC1 8 HOH A 503 HOH A 504 HOH A 536 HOH A 561 CRYST1 45.800 47.800 107.200 90.00 90.00 90.00 P 21 21 21 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 0.021834 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020921 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009328 0.00000