3DFR - Header Asymmetric Unit

HEADER OXIDO-REDUCTASE 25-JUN-82 3DFR

TITLE CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS TITLE 2 CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS TITLE 3 RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.1.3; COMPND 5 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS CASEI; SOURCE 3 ORGANISM_TAXID: 1582

KEYWDS OXIDO-REDUCTASE

EXPDTA X-RAY DIFFRACTION

AUTHOR D.J.FILMAN,D.A.MATTHEWS,J.T.BOLIN,J.KRAUT

REVDAT 6 24-FEB-09 3DFR 1 VERSN REVDAT 5 01-APR-03 3DFR 1 JRNL REVDAT 4 31-JAN-84 3DFR 1 REMARK REVDAT 3 30-SEP-83 3DFR 1 REVDAT REVDAT 2 07-MAR-83 3DFR 2 JRNL REMARK CONECT REVDAT 1 21-OCT-82 3DFR 0

SPRSDE 21-OCT-82 3DFR 1DFR

JRNL AUTH J.T.BOLIN,D.J.FILMAN,D.A.MATTHEWS,R.C.HAMLIN, JRNL AUTH 2 J.KRAUT JRNL TITL CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND JRNL TITL 2 LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE JRNL TITL 3 REFINED AT 1.7 A RESOLUTION. I. GENERAL FEATURES JRNL TITL 4 AND BINDING OF METHOTREXATE. JRNL REF J.BIOL.CHEM. V. 257 13650 1982 JRNL REFN ISSN 0021-9258 JRNL PMID 6815178

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.J.FILMAN,J.T.BOLIN,D.A.MATTHEWS,J.KRAUT REMARK 1 TITL CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND REMARK 1 TITL 2 LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REMARK 1 TITL 3 REFINED AT 1.7 ANGSTROMS RESOLUTION. II. REMARK 1 TITL 4 ENVIRONMENT OF BOUND NADPH AND IMPLICATIONS FOR REMARK 1 TITL 5 CATALYSIS REMARK 1 REF J.BIOL.CHEM. V. 257 13663 1982 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.W.VOLZ,D.A.MATTHEWS,R.A.ALDEN,S.T.FREER,C.HANSCH, REMARK 1 AUTH 2 B.T.KAUFMAN,J.KRAUT REMARK 1 TITL CRYSTAL STRUCTURE OF AVIAN DIHYDROFOLATE REDUCTASE REMARK 1 TITL 2 CONTAINING PHENYLTRIAZINE AND NADPH REMARK 1 REF J.BIOL.CHEM. V. 257 2528 1982 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.A.MATTHEWS REMARK 1 TITL INTERPRETATION OF NUCLEAR MAGNETIC RESONANCE REMARK 1 TITL 2 SPECTRA FOR LACTOBACILLUS CASEI DIHYDROFOLATE REMARK 1 TITL 3 REDUCTASE BASED ON THE X-RAY STRUCTURE OF THE REMARK 1 TITL 4 ENZYME-METHOTREXATE-NADPH COMPLEX REMARK 1 REF BIOCHEMISTRY V. 18 1602 1979 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 4 REMARK 1 AUTH D.A.MATTHEWS,R.A.ALDEN,S.T.FREER,N.-H.XUONG,J.KRAUT REMARK 1 TITL DIHYDROFOLATE REDUCTASE FROM LACTOBACILLUS CASEI. REMARK 1 TITL 2 STEREOCHEMISTRY OF NADPH BINDING REMARK 1 REF J.BIOL.CHEM. V. 254 4144 1979 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 5 REMARK 1 AUTH D.A.MATTHEWS,R.A.ALDEN,J.T.BOLIN,D.J.FILMAN, REMARK 1 AUTH 2 S.T.FREER,R.HAMLIN,W.G.J.HOL,R.L.KISLIUK, REMARK 1 AUTH 3 E.J.PASTORE,L.T.PLANTE,N.-H.XUONG,J.KRAUT REMARK 1 TITL DIHYDROFOLATE REDUCTASE FROM LACTOBACILLUS CASEI. REMARK 1 TITL 2 X-RAY STRUCTURE OF THE ENZYME-METHOTREXATE-NADPH REMARK 1 TITL 3 COMPLEX REMARK 1 REF J.BIOL.CHEM. V. 253 6946 1978 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 6 REMARK 1 AUTH D.A.MATTHEWS,R.A.ALDEN,J.T.BOLIN,S.T.FREER, REMARK 1 AUTH 2 R.HAMLIN,N.XUONG,J.KRAUT,M.POE,M.WILLIAMS, REMARK 1 AUTH 3 K.HOOGSTEEN REMARK 1 TITL DIHYDROFOLATE REDUCTASE. X-RAY STRUCTURE OF THE REMARK 1 TITL 2 BINARY COMPLEX WITH METHOTREXATE REMARK 1 REF SCIENCE V. 197 452 1977 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 7 REMARK 1 AUTH T.C.CRUSBERG,R.LEARY,R.L.KISLIUK REMARK 1 TITL PROPERTIES OF THYMIDYLATE SYNTHETASE FROM REMARK 1 TITL 2 DICHLOROMETHOTREXATE-RESISTANT LACTOBACILLUS CASEI REMARK 1 REF J.BIOL.CHEM. V. 245 5292 1970 REMARK 1 REFN ISSN 0021-9258

REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL 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 : 1294 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 264 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 3DFR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 67.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 31.12667 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 62.25333 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 46.69000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 77.81667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.56333 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 LYS A 51 CG CD CE NZ

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 PHE A 3 CG PHE A 3 CD1 0.114 REMARK 500 ARG A 9 CG ARG A 9 CD 0.167 REMARK 500 ARG A 9 CZ ARG A 9 NH1 0.088 REMARK 500 ARG A 9 CZ ARG A 9 NH2 0.093 REMARK 500 ASN A 10 CB ASN A 10 CG 0.227 REMARK 500 ASN A 10 CG ASN A 10 OD1 0.229 REMARK 500 GLY A 14 CA GLY A 14 C 0.117 REMARK 500 ASP A 16 CA ASP A 16 CB 0.150 REMARK 500 GLY A 17 N GLY A 17 CA 0.113 REMARK 500 HIS A 18 CG HIS A 18 ND1 0.139 REMARK 500 HIS A 18 NE2 HIS A 18 CD2 0.199 REMARK 500 LEU A 19 C LEU A 19 O -0.130 REMARK 500 PRO A 20 N PRO A 20 CA 0.120 REMARK 500 PRO A 20 CD PRO A 20 N 0.182 REMARK 500 LEU A 19 C PRO A 20 N 0.217 REMARK 500 HIS A 22 CG HIS A 22 CD2 0.116 REMARK 500 LEU A 23 C LEU A 23 O -0.141 REMARK 500 PRO A 24 CA PRO A 24 CB 0.118 REMARK 500 PRO A 24 CD PRO A 24 N 0.305 REMARK 500 LEU A 23 C PRO A 24 N 0.167 REMARK 500 HIS A 28 CG HIS A 28 CD2 0.161 REMARK 500 TYR A 29 CZ TYR A 29 CE2 0.078 REMARK 500 ARG A 31 NE ARG A 31 CZ 0.142 REMARK 500 ARG A 31 CZ ARG A 31 NH2 0.089 REMARK 500 ARG A 44 CD ARG A 44 NE -0.143 REMARK 500 ARG A 44 CZ ARG A 44 NH1 0.123 REMARK 500 ARG A 44 CZ ARG A 44 NH2 0.079 REMARK 500 TYR A 46 CG TYR A 46 CD1 0.080 REMARK 500 PHE A 49 CG PHE A 49 CD2 0.165 REMARK 500 PRO A 50 N PRO A 50 CA 0.125 REMARK 500 PRO A 50 CA PRO A 50 CB 0.154 REMARK 500 PRO A 50 CD PRO A 50 N 0.309 REMARK 500 PHE A 49 C PRO A 50 N 0.158 REMARK 500 LYS A 51 CA LYS A 51 CB 0.152 REMARK 500 ARG A 52 N ARG A 52 CA 0.137 REMARK 500 PRO A 53 CD PRO A 53 N 0.210 REMARK 500 ARG A 52 C PRO A 53 N 0.305 REMARK 500 PRO A 55 CD PRO A 55 N 0.213 REMARK 500 LEU A 54 C PRO A 55 N 0.234 REMARK 500 GLU A 56 CB GLU A 56 CG 0.155 REMARK 500 GLU A 56 CD GLU A 56 OE1 0.079 REMARK 500 HIS A 64 CG HIS A 64 CD2 0.060 REMARK 500 HIS A 64 CG HIS A 64 ND1 -0.107 REMARK 500 GLN A 65 CD GLN A 65 NE2 0.173 REMARK 500 GLU A 66 CB GLU A 66 CG 0.126 REMARK 500 GLU A 66 CD GLU A 66 OE2 0.074 REMARK 500 ASP A 67 CA ASP A 67 CB 0.335 REMARK 500 ASP A 67 CG ASP A 67 OD1 0.249 REMARK 500 ASP A 67 CG ASP A 67 OD2 0.224 REMARK 500 TYR A 68 CE1 TYR A 68 CZ 0.092 REMARK 500 REMARK 500 THIS ENTRY HAS 104 BOND DEVIATIONS. 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 THR A 1 CA - CB - CG2 ANGL. DEV. = 9.0 DEGREES REMARK 500 PHE A 3 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 PHE A 3 CD1 - CG - CD2 ANGL. DEV. = -14.1 DEGREES REMARK 500 PHE A 3 CB - CG - CD1 ANGL. DEV. = 9.8 DEGREES REMARK 500 PHE A 3 CG - CD2 - CE2 ANGL. DEV. = 21.4 DEGREES REMARK 500 PHE A 3 CD1 - CE1 - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 TRP A 5 CE3 - CZ3 - CH2 ANGL. DEV. = 9.9 DEGREES REMARK 500 TRP A 5 CZ3 - CH2 - CZ2 ANGL. DEV. = -9.3 DEGREES REMARK 500 ASN A 8 CB - CA - C ANGL. DEV. = 14.1 DEGREES REMARK 500 ASN A 8 CA - C - O ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG A 9 CG - CD - NE ANGL. DEV. = -20.3 DEGREES REMARK 500 ARG A 9 CD - NE - CZ ANGL. DEV. = 42.2 DEGREES REMARK 500 ARG A 9 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASN A 10 OD1 - CG - ND2 ANGL. DEV. = 33.7 DEGREES REMARK 500 ASN A 10 CB - CG - OD1 ANGL. DEV. = -27.9 DEGREES REMARK 500 LEU A 12 CB - CG - CD1 ANGL. DEV. = -11.4 DEGREES REMARK 500 ASP A 16 CB - CG - OD1 ANGL. DEV. = 9.2 DEGREES REMARK 500 LEU A 19 CB - CG - CD1 ANGL. DEV. = -12.2 DEGREES REMARK 500 LEU A 19 CA - C - O ANGL. DEV. = 19.7 DEGREES REMARK 500 PRO A 20 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 PRO A 20 CB - CA - C ANGL. DEV. = -13.6 DEGREES REMARK 500 LEU A 19 CA - C - N ANGL. DEV. = -17.1 DEGREES REMARK 500 PRO A 20 C - N - CA ANGL. DEV. = -15.3 DEGREES REMARK 500 PRO A 20 C - N - CD ANGL. DEV. = 24.1 DEGREES REMARK 500 TRP A 21 CB - CG - CD2 ANGL. DEV. = -12.7 DEGREES REMARK 500 TRP A 21 CB - CG - CD1 ANGL. DEV. = 14.0 DEGREES REMARK 500 PRO A 20 O - C - N ANGL. DEV. = -10.2 DEGREES REMARK 500 HIS A 22 CA - C - O ANGL. DEV. = 17.4 DEGREES REMARK 500 LEU A 23 CA - C - O ANGL. DEV. = 14.3 DEGREES REMARK 500 HIS A 22 CA - C - N ANGL. DEV. = -14.0 DEGREES REMARK 500 PRO A 24 CA - N - CD ANGL. DEV. = -12.9 DEGREES REMARK 500 LEU A 23 CA - C - N ANGL. DEV. = -19.3 DEGREES REMARK 500 PRO A 24 C - N - CA ANGL. DEV. = -12.1 DEGREES REMARK 500 PRO A 24 C - N - CD ANGL. DEV. = 25.5 DEGREES REMARK 500 ASP A 25 OD1 - CG - OD2 ANGL. DEV. = -15.7 DEGREES REMARK 500 ASP A 25 CB - CG - OD1 ANGL. DEV. = 14.4 DEGREES REMARK 500 PRO A 24 CA - C - N ANGL. DEV. = 15.6 DEGREES REMARK 500 ASP A 26 CB - CG - OD1 ANGL. DEV. = 8.5 DEGREES REMARK 500 ASP A 26 CA - C - O ANGL. DEV. = 13.2 DEGREES REMARK 500 LEU A 27 CA - C - O ANGL. DEV. = -13.5 DEGREES REMARK 500 ASP A 26 O - C - N ANGL. DEV. = -14.8 DEGREES REMARK 500 HIS A 28 CB - CG - CD2 ANGL. DEV. = -12.1 DEGREES REMARK 500 TYR A 29 CB - CG - CD2 ANGL. DEV. = 8.7 DEGREES REMARK 500 TYR A 29 CD1 - CG - CD2 ANGL. DEV. = -9.0 DEGREES REMARK 500 TYR A 29 CG - CD1 - CE1 ANGL. DEV. = 6.7 DEGREES REMARK 500 TYR A 29 CG - CD2 - CE2 ANGL. DEV. = 10.2 DEGREES REMARK 500 TYR A 29 CZ - CE2 - CD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 HIS A 28 CA - C - N ANGL. DEV. = 16.0 DEGREES REMARK 500 PHE A 30 CB - CG - CD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 31 CG - CD - NE ANGL. DEV. = 13.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 270 ANGLE DEVIATIONS. 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 HIS A 89 -113.71 -100.97 REMARK 500 LEU A 90 -67.47 132.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 9 0.07 SIDE_CHAIN REMARK 500 ARG A 31 0.19 SIDE_CHAIN REMARK 500 ARG A 44 0.09 SIDE_CHAIN REMARK 500 ARG A 52 0.12 SIDE_CHAIN REMARK 500 ARG A 57 0.15 SIDE_CHAIN 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 TRP A 21 -11.24 REMARK 500 ASP A 78 -12.18 REMARK 500 GLU A 145 10.90 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 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: (11X,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 ARG A 52 48.6 L L OUTSIDE RANGE REMARK 500 ASP A 78 45.6 L L OUTSIDE RANGE REMARK 500 GLN A 88 21.6 L L OUTSIDE RANGE REMARK 500 HIS A 89 -0.8 L D EXPECTING SP3 REMARK 500 LEU A 90 13.6 L L OUTSIDE RANGE REMARK 500 ASP A 109 46.4 L L OUTSIDE RANGE REMARK 500 LEU A 151 21.4 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): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 337 DISTANCE = 5.17 ANGSTROMS REMARK 525 HOH A 339 DISTANCE = 7.15 ANGSTROMS REMARK 525 HOH A 343 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH A 359 DISTANCE = 7.23 ANGSTROMS REMARK 525 HOH A 360 DISTANCE = 5.38 ANGSTROMS REMARK 525 HOH A 388 DISTANCE = 5.78 ANGSTROMS REMARK 525 HOH A 421 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH A 433 DISTANCE = 5.51 ANGSTROMS REMARK 525 HOH A 438 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH A 446 DISTANCE = 5.76 ANGSTROMS REMARK 525 HOH A 458 DISTANCE = 7.00 ANGSTROMS REMARK 525 HOH A 485 DISTANCE = 7.41 ANGSTROMS REMARK 525 HOH A 511 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A 521 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH A 525 DISTANCE = 8.59 ANGSTROMS REMARK 525 HOH A 535 DISTANCE = 6.97 ANGSTROMS REMARK 525 HOH A 607 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH A 622 DISTANCE = 6.22 ANGSTROMS

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: NDN REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE ADENINE BASE OF REMARK 800 THE NADPH COFACTOR REMARK 800 SITE_IDENTIFIER: NAR REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE ADENINE REMARK 800 MONONUCLEOTIDE RIBOSE OF THE NADPH COFACTOR REMARK 800 SITE_IDENTIFIER: NPP REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE PYROPHOSPHATE REMARK 800 OF THE NADPH COFACTOR REMARK 800 SITE_IDENTIFIER: NMR REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE NICOTINAMIDE REMARK 800 MONONUCLEOTIDE RIBOSE OF THE NADPH COFACTOR REMARK 800 SITE_IDENTIFIER: NND REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE NICOTINAMIDE REMARK 800 BASE OF THE NADPH COFACTOR REMARK 800 SITE_IDENTIFIER: MPT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE PTERIDINE OF REMARK 800 THE METHOTREXATE INHIBITOR REMARK 800 SITE_IDENTIFIER: MNM REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE N(10) METHYL OF REMARK 800 THE METHOTREXATE INHIBITOR REMARK 800 SITE_IDENTIFIER: MAB REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE P-AMINOBENZOYL REMARK 800 OF THE METHOTREXATE INHIBITOR REMARK 800 SITE_IDENTIFIER: MGL REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE GLUTAMATE OF REMARK 800 THE METHOTREXATE INHIBITOR REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 163 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTX A 164

DBREF 3DFR A 1 162 UNP P00381 DYR_LACCA 1 162

SEQADV 3DFR ASN A 8 UNP P00381 ASP 8 CONFLICT SEQADV 3DFR ASN A 10 UNP P00381 ASP 10 CONFLICT SEQADV 3DFR LEU A 90 UNP P00381 PRO 90 CONFLICT

SEQRES 1 A 162 THR ALA PHE LEU TRP ALA GLN ASN ARG ASN GLY LEU ILE SEQRES 2 A 162 GLY LYS ASP GLY HIS LEU PRO TRP HIS LEU PRO ASP ASP SEQRES 3 A 162 LEU HIS TYR PHE ARG ALA GLN THR VAL GLY LYS ILE MET SEQRES 4 A 162 VAL VAL GLY ARG ARG THR TYR GLU SER PHE PRO LYS ARG SEQRES 5 A 162 PRO LEU PRO GLU ARG THR ASN VAL VAL LEU THR HIS GLN SEQRES 6 A 162 GLU ASP TYR GLN ALA GLN GLY ALA VAL VAL VAL HIS ASP SEQRES 7 A 162 VAL ALA ALA VAL PHE ALA TYR ALA LYS GLN HIS LEU ASP SEQRES 8 A 162 GLN GLU LEU VAL ILE ALA GLY GLY ALA GLN ILE PHE THR SEQRES 9 A 162 ALA PHE LYS ASP ASP VAL ASP THR LEU LEU VAL THR ARG SEQRES 10 A 162 LEU ALA GLY SER PHE GLU GLY ASP THR LYS MET ILE PRO SEQRES 11 A 162 LEU ASN TRP ASP ASP PHE THR LYS VAL SER SER ARG THR SEQRES 12 A 162 VAL GLU ASP THR ASN PRO ALA LEU THR HIS THR TYR GLU SEQRES 13 A 162 VAL TRP GLN LYS LYS ALA

HET NDP A 163 48 HET MTX A 164 33

HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM MTX METHOTREXATE

FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 MTX C20 H22 N8 O5 FORMUL 4 HOH *264(H2 O)

HELIX 1 HB LEU A 23 THR A 34 1 12 HELIX 2 HC GLY A 42 PHE A 49 1 8 HELIX 3 HE ASP A 78 HIS A 89 1 12 HELIX 4 HF GLY A 99 LYS A 107 1 9

SHEET 1 S1 8 VAL A 74 VAL A 76 0 SHEET 2 S1 8 GLU A 56 THR A 63 1 O ASN A 59 N VAL A 74 SHEET 3 S1 8 GLY A 36 GLY A 42 1 O LYS A 37 N THR A 58 SHEET 4 S1 8 GLU A 93 GLY A 98 1 O GLU A 93 N ILE A 38 SHEET 5 S1 8 THR A 1 GLN A 7 1 N ALA A 2 O LEU A 94 SHEET 6 S1 8 ASP A 111 ALA A 119 1 O THR A 112 N PHE A 3 SHEET 7 S1 8 THR A 152 LYS A 161 -1 N LYS A 160 O ASP A 111 SHEET 8 S1 8 ASP A 135 VAL A 144 -1 N THR A 137 O GLN A 159

CISPEP 1 ARG A 52 PRO A 53 0 -8.17 CISPEP 2 GLY A 98 GLY A 99 0 2.29

SITE 1 NDN 8 LEU A 62 THR A 63 HIS A 64 HIS A 77 SITE 2 NDN 8 GLN A 101 ILE A 102 HOH A 279 HOH A 318 SITE 1 NAR 9 GLY A 42 ARG A 43 ARG A 44 THR A 63 SITE 2 NAR 9 HIS A 64 GLN A 65 GLN A 101 ILE A 102 SITE 3 NAR 9 HOH A 401 SITE 1 NPP 7 ARG A 44 THR A 45 GLY A 99 GLN A 101 SITE 2 NPP 7 ILE A 102 THR A 126 HOH A 301 SITE 1 NMR 7 ILE A 13 GLY A 14 HIS A 18 SER A 48 SITE 2 NMR 7 GLY A 99 HOH A 208 HOH A 439 SITE 1 NND 12 TRP A 5 ALA A 6 ILE A 13 LEU A 19 SITE 2 NND 12 TRP A 21 THR A 45 ALA A 97 GLY A 98 SITE 3 NND 12 GLY A 99 PHE A 103 MTX A 164 HOH A 439 SITE 1 MPT 14 LEU A 4 TRP A 5 ALA A 6 LEU A 19 SITE 2 MPT 14 TRP A 21 ASP A 26 LEU A 27 PHE A 30 SITE 3 MPT 14 ALA A 97 THR A 116 NDP A 163 HOH A 201 SITE 4 MPT 14 HOH A 217 HOH A 253 SITE 1 MNM 2 LEU A 19 SER A 48 SITE 1 MAB 5 LEU A 27 PHE A 30 PHE A 49 PRO A 50 SITE 2 MAB 5 LEU A 54 SITE 1 MGL 6 LEU A 27 HIS A 28 PHE A 30 ARG A 31 SITE 2 MGL 6 LEU A 54 ARG A 57 SITE 1 AC1 34 TRP A 5 ALA A 6 ILE A 13 GLY A 14 SITE 2 AC1 34 LYS A 15 GLY A 17 HIS A 18 LEU A 19 SITE 3 AC1 34 GLY A 42 ARG A 43 ARG A 44 THR A 45 SITE 4 AC1 34 LEU A 62 THR A 63 HIS A 64 GLN A 65 SITE 5 AC1 34 HIS A 77 ALA A 97 GLY A 99 ALA A 100 SITE 6 AC1 34 GLN A 101 ILE A 102 MTX A 164 HOH A 208 SITE 7 AC1 34 HOH A 276 HOH A 279 HOH A 301 HOH A 302 SITE 8 AC1 34 HOH A 318 HOH A 326 HOH A 373 HOH A 401 SITE 9 AC1 34 HOH A 439 HOH A 579 SITE 1 AC2 21 LEU A 4 TRP A 5 LEU A 19 ASP A 26 SITE 2 AC2 21 LEU A 27 HIS A 28 PHE A 30 ARG A 31 SITE 3 AC2 21 SER A 48 PHE A 49 PRO A 50 ARG A 57 SITE 4 AC2 21 ALA A 97 THR A 116 NDP A 163 HOH A 322 SITE 5 AC2 21 HOH A 329 HOH A 331 HOH A 559 HOH A 606 SITE 6 AC2 21 HOH A 621

CRYST1 71.860 71.860 93.380 90.00 90.00 120.00 P 61 6

ORIGX1 0.013916 0.008034 0.000000 0.00000

ORIGX2 0.000000 0.016069 0.000000 0.00000

ORIGX3 0.000000 0.000000 0.010709 0.00000

SCALE1 0.013916 0.008034 0.000000 0.00000

SCALE2 0.000000 0.016069 0.000000 0.00000

SCALE3 0.000000 0.000000 0.010709 0.00000