PDB Short entry for 2W3W HEADER OXIDOREDUCTASE 16-NOV-08 2W3W TITLE MYCOBACTERIUM AVIUM DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND A TITLE 2 LIPOPHILIC ANTIFOLATE SELECTIVE FOR M. AVIUM DHFR, 6-((2,5- TITLE 3 DIETHOXYPHENYL)AMINOMETHYL)-2,4-DIAMINO-5-METHYLPYRIDO(2,3-D) TITLE 4 PYRIMIDINE (SRI-8686) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES, 1-167; COMPND 5 EC: 1.5.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM AVIUM; SOURCE 3 ORGANISM_TAXID: 1764; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET11A; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A-MACDHFR-DEL; SOURCE 9 OTHER_DETAILS: STRAIN OBTAINED FROM THE AIDS RESEARCH AND REFERENCE SOURCE 10 REAGENT PROGRAM, DIVISION OF AIDS, NIAID, NIH, CATALOG NUMBER 1786. KEYWDS NONCLASSICAL ANTIFOLATES, ONE-CARBON METABOLISM, LIPOPHILIC KEYWDS 2 ANTIFOLATES, NADP, REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.K.W.LEUNG,R.C.REYNOLDS,D.W.BORHANI REVDAT 4 08-MAY-19 2W3W 1 REMARK REVDAT 3 06-MAR-19 2W3W 1 REMARK REVDAT 2 13-JUL-11 2W3W 1 VERSN REVDAT 1 17-NOV-09 2W3W 0 JRNL AUTH A.K.W.LEUNG,L.J.ROSS,S.ZYWNO-VAN GINKEL,R.C.REYNOLDS, JRNL AUTH 2 L.E.SEITZ,V.PATHAK,W.W.BARROW,E.L.WHITE,W.J.SULING, JRNL AUTH 3 J.R.PIPER,D.W.BORHANI JRNL TITL STRUCTURAL BASIS FOR SELECTIVE INHIBITION OF MYCOBACTERIUM JRNL TITL 2 AVIUM DIHYDROFOLATE REDUCTASE BY A LIPOPHILIC ANTIFOLATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 83.3 REMARK 3 NUMBER OF REFLECTIONS : 17339 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 920 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 545 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1247 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 18.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.89000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : -0.70000 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): 0.110 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.279 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1430 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 975 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1971 ; 1.664 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2335 ; 1.310 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 179 ; 5.915 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 54 ;30.685 ;20.741 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 208 ;12.814 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;19.991 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 211 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1613 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 310 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 231 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1065 ; 0.215 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 677 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 789 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 97 ; 0.137 ; 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): 11 ; 0.175 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 30 ; 0.277 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.224 ; 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): 1098 ; 1.265 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1390 ; 1.438 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 708 ; 2.408 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 581 ; 3.377 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 166 REMARK 3 ORIGIN FOR THE GROUP (A): 13.8920 2.3950 46.6300 REMARK 3 T TENSOR REMARK 3 T11: -0.0861 T22: -0.0501 REMARK 3 T33: -0.0225 T12: -0.0208 REMARK 3 T13: -0.0056 T23: 0.0158 REMARK 3 L TENSOR REMARK 3 L11: 1.1401 L22: 1.5339 REMARK 3 L33: 3.8496 L12: -0.1259 REMARK 3 L13: 0.2162 L23: 1.0122 REMARK 3 S TENSOR REMARK 3 S11: 0.0235 S12: -0.0003 S13: 0.0006 REMARK 3 S21: 0.0573 S22: 0.0297 S23: -0.0504 REMARK 3 S31: 0.1210 S32: -0.1365 S33: -0.0532 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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. NOTE THAT THE 2' ETHYL GROUP OF SRI-8686 (VG9) WAS REMARK 3 NOT LOCATED IN ELECTRON DENSITY MAPS. APPROXIMATE COORDINATES REMARK 3 FOR THESE TWO ATOMS ARE INCLUDED, BUT AT ZERO OCCUPANCY. REMARK 4 REMARK 4 2W3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1290038124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS UNIVERSITY BRANDEIS B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18299 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -10.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 37.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: UNPUBLISHED M. AVIUM DHFR-NADPH- TRIMETHOPRIM REMARK 200 COMPLEX, SINCE DEPOSITED AS PDB ENTRY 2W3V. REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAVDHFR (15 MG/ML) IN 20 MM HEPES (PH REMARK 280 7.0), 1 MM DTT, 0.1 MM EDTA, 1.5 MM NAN3 WAS MIXED WITH NADPH (3 REMARK 280 MM, 15 MIN AT ROOM TEMPERATURE) AND THEN SRI-8686 (2 MM, 15 MIN REMARK 280 ON ICE). CRYSTALLIZATION (HANGING DROP VAPOR PHASE EQUILIBRATION) REMARK 280 WAS ACHIEVED BY MIXING WITH AN EQUAL VOLUME OF THE PROTEIN REMARK 280 COMPLEX WITH A RESERVOIR SOLUTION CONSISTING OF 55-70% 2-METHYL- REMARK 280 2, 4-PENTANEDIOL (MPD) AND 100 MM HEPES (PH 6.5-7.5), AND REMARK 280 SUSPENDING THE MIXTURE OVER THE RESERVOIR AT 277 K. SMALL ROD- REMARK 280 LIKE CRYSTALS (0.01 X 0.01 X 0.05 MM) GREW WITHIN 2 DAYS. REMARK 280 CRYSTALS WERE FLASH-COOLED DIRECTLY FROM THE DROP IN LIQUID N2., REMARK 280 VAPOR DIFFUSION, HANGING DROP 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 18.36450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.59550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.98250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.59550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.36450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.98250 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 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 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 465 THR A 2 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 ARG A 3 CD NE CZ NH1 NH2 REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 GLU A 78 CD OE1 OE2 REMARK 470 ARG A 81 CD NE CZ NH1 NH2 REMARK 470 ASP A 126 CG OD1 OD2 REMARK 470 ARG A 128 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 167 CA C O CB CG OD1 OD2 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 OD2 ASP A 23 O HOH A 2015 2.14 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 PRO A 25 39.00 -90.26 REMARK 500 ALA A 98 74.90 -150.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 6-((2,5-DIETHOXYPHENYL)AMINOMETHYL)-2,4-DIAMINO-5- REMARK 600 6-((2,5-DIETHOXYPHENYL)AMINOMETHYL)-2, REMARK 600 4-DIAMINO-5-METHYLPYRIDO(2,3-D)PYRIMIDINE (VG9): LIGAND IS REMARK 600 ALSO KNOWN AS SRI-8686. NOTE THAT THE 2' ETHYL GROUP OF REMARK 600 SRI-8686 WAS NOT LOCATED IN ELECTRON DENSITY MAPS. REMARK 600 APPROXIMATE COORDINATES FOR THESE TWO ATOMS ARE INCLUDED, REMARK 600 BUT AT ZERO OCCUPANCY. REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 VG9 A 1168 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VG9 A 1168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 1169 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W3V RELATED DB: PDB REMARK 900 MYCOBACTERIUM AVIUM DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH REMARK 900 AND TRIMETHOPRIM REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 168-181 OF WILDTYPE M. AVIUM DHFR WERE DELETED IN REMARK 999 THE EXPRESSION CONSTRUCT. THE FIRST ELEVEN CODONS OF THE M. REMARK 999 AVIUM DHFR READING FRAME WERE MUTATED TO INCREASE THE A REMARK 999 AND T CONTENT. THE CODONS USED WERE 5'-ATG-ACT-CGT-GCT-GAA- REMARK 999 GTA-GGT-CTG-GTA-TGG-GCT. PCR INTRODUCED AN UNINTENDED REMARK 999 SILENT MUTATION AT VAL120 (GTC MUTATED TO GTT). DBREF 2W3W A 1 167 UNP O30463 O30463_MYCAV 1 167 SEQRES 1 A 167 MET THR ARG ALA GLU VAL GLY LEU VAL TRP ALA GLN SER SEQRES 2 A 167 THR SER GLY VAL ILE GLY ARG GLY GLY ASP ILE PRO TRP SEQRES 3 A 167 SER VAL PRO GLU ASP LEU THR ARG PHE LYS GLU VAL THR SEQRES 4 A 167 MET GLY HIS THR VAL ILE MET GLY ARG ARG THR TRP GLU SEQRES 5 A 167 SER LEU PRO ALA LYS VAL ARG PRO LEU PRO GLY ARG ARG SEQRES 6 A 167 ASN VAL VAL VAL SER ARG ARG PRO ASP PHE VAL ALA GLU SEQRES 7 A 167 GLY ALA ARG VAL ALA GLY SER LEU GLU ALA ALA LEU ALA SEQRES 8 A 167 TYR ALA GLY SER ASP PRO ALA PRO TRP VAL ILE GLY GLY SEQRES 9 A 167 ALA GLN ILE TYR LEU LEU ALA LEU PRO HIS ALA THR ARG SEQRES 10 A 167 CYS GLU VAL THR GLU ILE GLU ILE ASP LEU ARG ARG ASP SEQRES 11 A 167 ASP ASP ASP ALA LEU ALA PRO ALA LEU ASP ASP SER TRP SEQRES 12 A 167 VAL GLY GLU THR GLY GLU TRP LEU ALA SER ARG SER GLY SEQRES 13 A 167 LEU ARG TYR ARG PHE HIS SER TYR ARG ARG ASP HET VG9 A1168 27 HET NDP A1169 48 HETNAM VG9 6-{[(2,5-DIETHOXYPHENYL)AMINO]METHYL}-5-METHYLPYRIDO[2, HETNAM 2 VG9 3-D]PYRIMIDINE-2,4-DIAMINE HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE FORMUL 2 VG9 C19 H24 N6 O2 FORMUL 3 NDP C21 H30 N7 O17 P3 FORMUL 4 HOH *126(H2 O) HELIX 1 1 VAL A 28 MET A 40 1 13 HELIX 2 2 ARG A 48 LEU A 54 1 7 HELIX 3 3 PRO A 55 ARG A 59 5 5 HELIX 4 4 SER A 85 ALA A 93 1 9 HELIX 5 5 GLY A 104 LEU A 112 1 9 HELIX 6 6 PRO A 113 ALA A 115 5 3 SHEET 1 AA 8 ARG A 81 ALA A 83 0 SHEET 2 AA 8 ARG A 65 VAL A 69 1 O ASN A 66 N ARG A 81 SHEET 3 AA 8 THR A 43 GLY A 47 1 O VAL A 44 N VAL A 67 SHEET 4 AA 8 TRP A 100 GLY A 103 1 O TRP A 100 N ILE A 45 SHEET 5 AA 8 GLY A 7 SER A 13 1 O GLY A 7 N VAL A 101 SHEET 6 AA 8 ARG A 117 GLU A 124 1 O ARG A 117 N LEU A 8 SHEET 7 AA 8 ARG A 158 ARG A 165 -1 O ARG A 158 N GLU A 124 SHEET 8 AA 8 VAL A 144 THR A 147 -1 O VAL A 144 N ARG A 165 SHEET 1 AB 8 ARG A 81 ALA A 83 0 SHEET 2 AB 8 ARG A 65 VAL A 69 1 O ASN A 66 N ARG A 81 SHEET 3 AB 8 THR A 43 GLY A 47 1 O VAL A 44 N VAL A 67 SHEET 4 AB 8 TRP A 100 GLY A 103 1 O TRP A 100 N ILE A 45 SHEET 5 AB 8 GLY A 7 SER A 13 1 O GLY A 7 N VAL A 101 SHEET 6 AB 8 ARG A 117 GLU A 124 1 O ARG A 117 N LEU A 8 SHEET 7 AB 8 ARG A 158 ARG A 165 -1 O ARG A 158 N GLU A 124 SHEET 8 AB 8 LEU A 151 ALA A 152 -1 O LEU A 151 N TYR A 159 SHEET 1 AC 2 VAL A 17 GLY A 19 0 SHEET 2 AC 2 ALA A 134 LEU A 135 -1 O ALA A 134 N ILE A 18 CISPEP 1 ARG A 59 PRO A 60 0 -3.80 CISPEP 2 GLY A 103 GLY A 104 0 6.76 SITE 1 AC1 11 VAL A 9 TRP A 10 ALA A 11 ILE A 24 SITE 2 AC1 11 ASP A 31 LEU A 32 PHE A 35 ILE A 102 SITE 3 AC1 11 TYR A 108 NDP A1169 HOH A2087 SITE 1 AC2 31 TRP A 10 ALA A 11 ILE A 18 GLY A 19 SITE 2 AC2 31 GLY A 22 ASP A 23 ILE A 24 GLY A 47 SITE 3 AC2 31 ARG A 48 ARG A 49 THR A 50 VAL A 69 SITE 4 AC2 31 SER A 70 ARG A 71 ARG A 72 GLY A 84 SITE 5 AC2 31 ILE A 102 GLY A 104 ALA A 105 GLN A 106 SITE 6 AC2 31 ILE A 107 TYR A 108 LEU A 110 VG9 A1168 SITE 7 AC2 31 HOH A2048 HOH A2121 HOH A2122 HOH A2123 SITE 8 AC2 31 HOH A2124 HOH A2125 HOH A2126 CRYST1 36.729 53.965 81.191 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 0.027226 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012317 0.00000