HEADER OXIDOREDUCTASE 22-MAY-08 3D80 TITLE STRUCTURAL ANALYSIS OF A HOLO ENZYME COMPLEX OF MOUSE DIHYDROFOLATE TITLE 2 REDUCTASE WITH NADPH AND A TERNARY COMPLEX WTIH THE POTENT AND TITLE 3 SELECTIVE INHIBITOR 2,4-DIAMINO-6-(2'-HYDROXYDIBENZ[B,F]AZEPIN-5-YL) TITLE 4 METHYLPTERIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MOUSE DIHDYROFOLATE REDUCTASE; COMPND 5 EC: 1.5.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: JM105; SOURCE 6 GENE: DHFR; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPH70D KEYWDS MOUSE HOLO ENZYME TERNARY LIGAND COMPLEX DIHYDROFOLATE REDUCTASE, KEYWDS 2 NADP, ONE-CARBON METABOLISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.CODY REVDAT 5 30-AUG-23 3D80 1 REMARK REVDAT 4 12-JUN-13 3D80 1 HETATM REVDAT 3 13-JUL-11 3D80 1 VERSN REVDAT 2 24-FEB-09 3D80 1 VERSN REVDAT 1 23-SEP-08 3D80 0 JRNL AUTH V.CODY,J.PACE,A.ROSOWSKY JRNL TITL STRUCTURAL ANALYSIS OF A HOLOENZYME COMPLEX OF MOUSE JRNL TITL 2 DIHYDROFOLATE REDUCTASE WITH NADPH AND A TERNARY COMPLEX JRNL TITL 3 WITH THE POTENT AND SELECTIVE INHIBITOR JRNL TITL 4 2,4-DIAMINO-6-(2'-HYDROXYDIBENZ[B,F]AZEPIN-5-YL) JRNL TITL 5 METHYLPTERIDINE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 977 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18703847 JRNL DOI 10.1107/S0907444908022348 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 35455 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1851 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2578 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1513 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 95 REMARK 3 SOLVENT ATOMS : 316 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.077 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.370 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1724 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2353 ; 1.682 ; 2.048 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 207 ; 5.633 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;33.902 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 309 ;14.215 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;14.526 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 251 ; 0.374 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1298 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 828 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1160 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 239 ; 0.167 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 46 ; 0.243 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 38 ; 0.179 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1001 ; 0.831 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1598 ; 1.375 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 855 ; 1.976 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 747 ; 2.963 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3D80 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000047707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35455 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 31.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 15.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : 0.02000 REMARK 200 FOR SHELL : 31.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2FZJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M TRIS, PH 8.3, 75 MM NA REMARK 280 CACODYLATE, PH 6.5, 21% PEG 4K, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.65000 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 150 CD 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 O2X NDP A 187 O HOH A 285 1.05 REMARK 500 O HOH A 286 O HOH A 522 1.19 REMARK 500 NE2 GLN A 35 O HOH A 523 1.26 REMARK 500 CB ALA A 106 O HOH A 407 1.63 REMARK 500 CB ALA A 106 O HOH A 524 1.68 REMARK 500 CB SER A 107 O HOH A 332 1.80 REMARK 500 OG SER A 119 O1N NDP A 187 1.98 REMARK 500 NH1 ARG A 132 O HOH A 494 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 320 O HOH A 565 2545 2.05 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 150 CG GLU A 150 CD 0.391 REMARK 500 GLU A 150 CD GLU A 150 OE1 0.626 REMARK 500 GLU A 150 CD GLU A 150 OE2 0.614 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 89 CA - CB - CG ANGL. DEV. = 15.0 DEGREES REMARK 500 LYS A 108 C - N - CA ANGL. DEV. = -20.5 DEGREES REMARK 500 GLU A 150 OE1 - CD - OE2 ANGL. DEV. = -16.1 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 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 110 -98.23 -97.29 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 GLU A 150 0.07 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 ANGLE, 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 GLU A 104 -10.77 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 NDP A 187 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE Q22 A 188 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 189 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 190 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 191 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FZJ RELATED DB: PDB REMARK 900 MOUSE DHFR REMARK 900 RELATED ID: 3D7X RELATED DB: PDB REMARK 900 RELATED ID: 3D7Y RELATED DB: PDB REMARK 900 RELATED ID: 3D84 RELATED DB: PDB DBREF 3D80 A 1 186 UNP P00375 DYR_MOUSE 2 187 SEQRES 1 A 186 VAL ARG PRO LEU ASN CYS ILE VAL ALA VAL SER GLN ASN SEQRES 2 A 186 MET GLY ILE GLY LYS ASN GLY ASP LEU PRO TRP PRO PRO SEQRES 3 A 186 LEU ARG ASN GLU PHE LYS TYR PHE GLN ARG MET THR THR SEQRES 4 A 186 THR SER SER VAL GLU GLY LYS GLN ASN LEU VAL ILE MET SEQRES 5 A 186 GLY ARG LYS THR TRP PHE SER ILE PRO GLU LYS ASN ARG SEQRES 6 A 186 PRO LEU LYS ASP ARG ILE ASN ILE VAL LEU SER ARG GLU SEQRES 7 A 186 LEU LYS GLU PRO PRO ARG GLY ALA HIS PHE LEU ALA LYS SEQRES 8 A 186 SER LEU ASP ASP ALA LEU ARG LEU ILE GLU GLN PRO GLU SEQRES 9 A 186 LEU ALA SER LYS VAL ASP MET VAL TRP ILE VAL GLY GLY SEQRES 10 A 186 SER SER VAL TYR GLN GLU ALA MET ASN GLN PRO GLY HIS SEQRES 11 A 186 LEU ARG LEU PHE VAL THR ARG ILE MET GLN GLU PHE GLU SEQRES 12 A 186 SER ASP THR PHE PHE PRO GLU ILE ASP LEU GLY LYS TYR SEQRES 13 A 186 LYS LEU LEU PRO GLU TYR PRO GLY VAL LEU SER GLU VAL SEQRES 14 A 186 GLN GLU GLU LYS GLY ILE LYS TYR LYS PHE GLU VAL TYR SEQRES 15 A 186 GLU LYS LYS ASP HET NDP A 187 48 HET Q22 A 188 29 HET GOL A 189 6 HET GOL A 190 6 HET GOL A 191 6 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM Q22 (4AS)-5-[(2,4-DIAMINOPTERIDIN-6-YL)METHYL]-4A,5- HETNAM 2 Q22 DIHYDRO-2H-DIBENZO[B,F]AZEPIN-8-OL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 Q22 C21 H19 N7 O FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 HOH *316(H2 O) HELIX 1 1 LEU A 27 THR A 40 1 14 HELIX 2 2 ARG A 54 ILE A 60 1 7 HELIX 3 3 PRO A 61 ARG A 65 5 5 HELIX 4 4 SER A 92 GLU A 101 1 10 HELIX 5 5 GLN A 102 VAL A 109 5 8 HELIX 6 6 GLY A 117 ASN A 126 1 10 SHEET 1 A 8 PHE A 88 ALA A 90 0 SHEET 2 A 8 ILE A 71 LEU A 75 1 N VAL A 74 O ALA A 90 SHEET 3 A 8 LEU A 49 GLY A 53 1 N VAL A 50 O ILE A 71 SHEET 4 A 8 VAL A 112 ILE A 114 1 O TRP A 113 N LEU A 49 SHEET 5 A 8 LEU A 4 VAL A 10 1 N ASN A 5 O ILE A 114 SHEET 6 A 8 LEU A 131 ILE A 138 1 O PHE A 134 N CYS A 6 SHEET 7 A 8 ILE A 175 LYS A 184 -1 O GLU A 180 N VAL A 135 SHEET 8 A 8 LYS A 157 LEU A 158 -1 N LYS A 157 O GLU A 183 SHEET 1 B 8 PHE A 88 ALA A 90 0 SHEET 2 B 8 ILE A 71 LEU A 75 1 N VAL A 74 O ALA A 90 SHEET 3 B 8 LEU A 49 GLY A 53 1 N VAL A 50 O ILE A 71 SHEET 4 B 8 VAL A 112 ILE A 114 1 O TRP A 113 N LEU A 49 SHEET 5 B 8 LEU A 4 VAL A 10 1 N ASN A 5 O ILE A 114 SHEET 6 B 8 LEU A 131 ILE A 138 1 O PHE A 134 N CYS A 6 SHEET 7 B 8 ILE A 175 LYS A 184 -1 O GLU A 180 N VAL A 135 SHEET 8 B 8 GLN A 170 GLU A 172 -1 N GLN A 170 O TYR A 177 SHEET 1 C 2 GLY A 15 GLY A 17 0 SHEET 2 C 2 THR A 146 PHE A 147 -1 O THR A 146 N ILE A 16 CISPEP 1 ARG A 65 PRO A 66 0 -6.75 CISPEP 2 ARG A 65 PRO A 66 0 -7.11 CISPEP 3 GLY A 116 GLY A 117 0 -0.76 SITE 1 AC1 32 VAL A 8 ALA A 9 ILE A 16 GLY A 17 SITE 2 AC1 32 GLY A 20 ASP A 21 LEU A 22 GLY A 53 SITE 3 AC1 32 ARG A 54 LYS A 55 THR A 56 LEU A 75 SITE 4 AC1 32 SER A 76 ARG A 77 GLU A 78 LYS A 91 SITE 5 AC1 32 SER A 92 VAL A 115 GLY A 117 SER A 118 SITE 6 AC1 32 SER A 119 THR A 146 Q22 A 188 HOH A 285 SITE 7 AC1 32 HOH A 302 HOH A 304 HOH A 313 HOH A 348 SITE 8 AC1 32 HOH A 388 HOH A 406 HOH A 449 HOH A 458 SITE 1 AC2 11 ILE A 7 VAL A 8 GLY A 20 ASP A 21 SITE 2 AC2 11 GLU A 30 PHE A 31 PHE A 34 VAL A 115 SITE 3 AC2 11 TYR A 121 THR A 136 NDP A 187 SITE 1 AC3 6 PRO A 82 PRO A 83 ARG A 84 GLY A 85 SITE 2 AC3 6 ALA A 86 HOH A 376 SITE 1 AC4 4 THR A 39 SER A 41 HOH A 330 HOH A 331 SITE 1 AC5 6 LYS A 80 PRO A 82 LEU A 89 HOH A 277 SITE 2 AC5 6 HOH A 353 HOH A 544 CRYST1 41.482 61.300 43.589 90.00 117.23 90.00 P 1 21 1 2 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 0.024107 0.000000 0.012403 0.00000 SCALE2 0.000000 0.016313 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025800 0.00000