HEADER LIGASE 22-JUN-09 3HY3 TITLE STRUCTURE OF HUMAN MTHFS WITH 10-FORMYLTETRAHYDROFOLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5,10-METHENYL-TETRAHYDROFOLATE SYNTHETASE, METHENYL-THF COMPND 5 SYNTHETASE, MTHFS; COMPND 6 EC: 6.3.3.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MTHFS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS ANTIFOLATE, CANCER, 10-FORMYLTETRAHYDROFOLATE, ATP-BINDING, FOLATE- KEYWDS 2 BINDING, LIGASE, MAGNESIUM, NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.WU,Y.LI,G.SONG,C.CHENG,N.SHAW,Z.-J.LIU REVDAT 5 01-NOV-23 3HY3 1 REMARK LINK REVDAT 4 13-JUL-11 3HY3 1 VERSN REVDAT 3 20-OCT-09 3HY3 1 JRNL REVDAT 2 28-JUL-09 3HY3 1 REMARK REVDAT 1 14-JUL-09 3HY3 0 JRNL AUTH D.WU,Y.LI,G.SONG,C.CHENG,R.ZHANG,A.JOACHIMIAK,N.SHAW, JRNL AUTH 2 Z.-J.LIU JRNL TITL STRUCTURAL BASIS FOR THE INHIBITION OF HUMAN JRNL TITL 2 5,10-METHENYLTETRAHYDROFOLATE SYNTHETASE BY N10-SUBSTITUTED JRNL TITL 3 FOLATE ANALOGUES JRNL REF CANCER RES. V. 69 7294 2009 JRNL REFN ISSN 0008-5472 JRNL PMID 19738041 JRNL DOI 10.1158/0008-5472.CAN-09-1927 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18978 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1027 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1362 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1521 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.59000 REMARK 3 B22 (A**2) : -0.32000 REMARK 3 B33 (A**2) : -1.27000 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): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.127 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.000 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.003 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.40 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: THE LIGAND 10F IN THIS ENTRY IS 10- REMARK 3 FORMYLTETRAHYDROFOLATE. HOWEVER, THERE IS SOME DISCREPANCY IN REMARK 3 THE GEOMETRY. THE GEOMETRY FOR 10F IS SUGGESTED BY THE REMARK 3 REFINEMENT. THE CO-ORDINATES FIT WELL IN THE ELECTRON DENSITY REMARK 3 MAP. THE MAP WAS GENERATED USING A DATASET COLLECTED AT 1.8 REMARK 3 ANGSTROM RESOLUTION. THE DENSITY FOR THE LIGAND IS UNAMBIGUOUS REMARK 3 AND THEREFORE THE GEOMETRIES ARE CORRECT AND ARE AS THEY WOULD REMARK 3 BE IN A BIOLOGICAL MOLECULE, WHERE THE MICRO ENVIRONMENT HAS A REMARK 3 PROFOUND INFLUENCE ON THE GEOMETRIES OF THE LIGAND. REMARK 4 REMARK 4 3HY3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053724. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23512 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3HXT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES, PH6.6, 20MM MGCL2.6H2O, REMARK 280 20MM NICL2.6H2O, 20% (W/V) PEG 3350, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 29.70400 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 29.70400 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 24.43050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.48700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.43050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.48700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.70400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.43050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.48700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 29.70400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.43050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.48700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PQS 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -154.0 KCAL/MOL 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 -29.70400 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 237 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 264 LIES ON A SPECIAL POSITION. 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 GLU A 187 REMARK 465 ASN A 188 REMARK 465 ASP A 199 REMARK 465 SER A 200 REMARK 465 SER A 201 REMARK 465 THR A 202 REMARK 465 ALA A 203 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 ALA A 2 CB REMARK 470 GLN A 19 CG CD OE1 NE2 REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 ARG A 29 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 38 CG CD OE1 NE2 REMARK 470 LYS A 50 CG CD CE NZ REMARK 470 GLN A 59 CG CD OE1 NE2 REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 LYS A 150 CG CD CE NZ REMARK 470 GLN A 162 CG CD OE1 NE2 REMARK 470 GLU A 165 CG CD OE1 OE2 REMARK 470 VAL A 166 CG1 CG2 REMARK 470 VAL A 185 CG1 CG2 REMARK 470 ASN A 186 CG OD1 ND2 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 324 O HOH A 348 2.08 REMARK 500 OE1 GLN A 182 O HOH A 297 2.12 REMARK 500 O GLU A 165 O HOH A 325 2.13 REMARK 500 O ASN A 88 O HOH A 239 2.18 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 246 O HOH A 295 1455 2.16 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 PHE A 133 CZ PHE A 133 CE2 0.122 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 LYS A 76 CD - CE - NZ ANGL. DEV. = -14.7 DEGREES REMARK 500 ARG A 145 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 LEU A 181 CB - CG - CD1 ANGL. DEV. = 10.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 10F A 501 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 205 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 NE2 REMARK 620 2 ASP A 91 OD2 90.4 REMARK 620 3 HOH A 292 O 168.1 89.1 REMARK 620 4 HOH A 296 O 109.7 80.7 82.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 204 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 290 O REMARK 620 2 HOH A 297 O 96.9 REMARK 620 3 HOH A 323 O 89.7 172.1 REMARK 620 4 HOH A 344 O 96.7 86.7 88.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 10F A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 214 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HXT RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN MTHFS, APO ENZYME REMARK 900 RELATED ID: 3HY4 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN MTHFS WITH N5-IMINIUM PHOSPHATE REMARK 900 RELATED ID: 3HY6 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN MTHFS WITH ADP DBREF 3HY3 A 1 203 UNP P49914 MTHFS_HUMAN 1 203 SEQRES 1 A 203 MET ALA ALA ALA ALA VAL SER SER ALA LYS ARG SER LEU SEQRES 2 A 203 ARG GLY GLU LEU LYS GLN ARG LEU ARG ALA MET SER ALA SEQRES 3 A 203 GLU GLU ARG LEU ARG GLN SER ARG VAL LEU SER GLN LYS SEQRES 4 A 203 VAL ILE ALA HIS SER GLU TYR GLN LYS SER LYS ARG ILE SEQRES 5 A 203 SER ILE PHE LEU SER MET GLN ASP GLU ILE GLU THR GLU SEQRES 6 A 203 GLU ILE ILE LYS ASP ILE PHE GLN ARG GLY LYS ILE CYS SEQRES 7 A 203 PHE ILE PRO ARG TYR ARG PHE GLN SER ASN HIS MET ASP SEQRES 8 A 203 MET VAL ARG ILE GLU SER PRO GLU GLU ILE SER LEU LEU SEQRES 9 A 203 PRO LYS THR SER TRP ASN ILE PRO GLN PRO GLY GLU GLY SEQRES 10 A 203 ASP VAL ARG GLU GLU ALA LEU SER THR GLY GLY LEU ASP SEQRES 11 A 203 LEU ILE PHE MET PRO GLY LEU GLY PHE ASP LYS HIS GLY SEQRES 12 A 203 ASN ARG LEU GLY ARG GLY LYS GLY TYR TYR ASP ALA TYR SEQRES 13 A 203 LEU LYS ARG CYS LEU GLN HIS GLN GLU VAL LYS PRO TYR SEQRES 14 A 203 THR LEU ALA LEU ALA PHE LYS GLU GLN ILE CYS LEU GLN SEQRES 15 A 203 VAL PRO VAL ASN GLU ASN ASP MET LYS VAL ASP GLU VAL SEQRES 16 A 203 LEU TYR GLU ASP SER SER THR ALA HET 10F A 501 34 HET NI A 204 1 HET NI A 205 1 HET MG A 206 1 HET MG A 207 1 HET MG A 208 1 HET MG A 209 1 HET MG A 210 1 HET MG A 211 1 HET MG A 212 1 HET MG A 213 1 HET MG A 214 1 HETNAM 10F N-({4-[{[(2R,4S,4AR,6S,8AS)-2-AMINO-4- HETNAM 2 10F HYDROXYDECAHYDROPTERIDIN-6-YL]METHYL}(FORMYL) HETNAM 3 10F AMINO]PHENYL}CARBONYL)-D-GLUTAMIC ACID HETNAM NI NICKEL (II) ION HETNAM MG MAGNESIUM ION FORMUL 2 10F C20 H29 N7 O7 FORMUL 3 NI 2(NI 2+) FORMUL 5 MG 9(MG 2+) FORMUL 14 HOH *137(H2 O) HELIX 1 1 MET A 1 ALA A 23 1 23 HELIX 2 2 SER A 25 ALA A 42 1 18 HELIX 3 3 HIS A 43 SER A 49 1 7 HELIX 4 4 THR A 64 ARG A 74 1 11 HELIX 5 5 SER A 97 SER A 102 1 6 HELIX 6 6 GLU A 122 THR A 126 5 5 HELIX 7 7 GLY A 151 LEU A 161 1 11 HELIX 8 8 PHE A 175 ILE A 179 5 5 SHEET 1 A 6 HIS A 89 ILE A 95 0 SHEET 2 A 6 ILE A 77 ARG A 84 -1 N ARG A 84 O HIS A 89 SHEET 3 A 6 ARG A 51 SER A 53 1 N ILE A 52 O ILE A 77 SHEET 4 A 6 LEU A 131 MET A 134 1 O PHE A 133 N SER A 53 SHEET 5 A 6 TYR A 169 LEU A 173 1 O TYR A 169 N ILE A 132 SHEET 6 A 6 GLU A 194 LEU A 196 1 O LEU A 196 N ALA A 172 SHEET 1 B 2 GLY A 138 PHE A 139 0 SHEET 2 B 2 ARG A 145 LEU A 146 -1 O LEU A 146 N GLY A 138 LINK NE2 HIS A 89 NI NI A 205 1555 1555 2.29 LINK OD2 ASP A 91 NI NI A 205 1555 1555 2.20 LINK NI NI A 204 O HOH A 290 1555 1555 2.18 LINK NI NI A 204 O HOH A 297 1555 1555 2.26 LINK NI NI A 204 O HOH A 323 1555 1555 2.41 LINK NI NI A 204 O HOH A 344 1555 1555 2.41 LINK NI NI A 205 O HOH A 292 1555 1555 2.28 LINK NI NI A 205 O HOH A 296 1555 1555 2.15 LINK MG MG A 212 O HOH A 311 1555 1555 2.38 SITE 1 AC1 14 PHE A 55 LEU A 56 MET A 58 GLU A 61 SITE 2 AC1 14 TYR A 83 PHE A 85 TRP A 109 ARG A 148 SITE 3 AC1 14 GLY A 149 LYS A 150 TYR A 152 HOH A 215 SITE 4 AC1 14 HOH A 230 HOH A 244 SITE 1 AC2 5 HIS A 142 HOH A 290 HOH A 297 HOH A 323 SITE 2 AC2 5 HOH A 344 SITE 1 AC3 5 HIS A 89 ASP A 91 HIS A 163 HOH A 292 SITE 2 AC3 5 HOH A 296 SITE 1 AC4 4 MET A 92 ALA A 123 LEU A 124 TYR A 156 SITE 1 AC5 3 THR A 107 SER A 108 HOH A 327 SITE 1 AC6 2 GLU A 16 HOH A 348 SITE 1 AC7 3 ARG A 84 PHE A 85 GLN A 86 SITE 1 AC8 3 CYS A 180 LEU A 181 HOH A 300 SITE 1 AC9 1 GLY A 15 SITE 1 BC1 2 ASP A 60 HOH A 311 SITE 1 BC2 4 HIS A 89 MET A 90 ARG A 159 HOH A 289 SITE 1 BC3 2 ARG A 74 LYS A 76 CRYST1 48.861 144.974 59.408 90.00 90.00 90.00 C 2 2 21 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 0.020466 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006898 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016833 0.00000