HEADER TRANSFERASE 12-FEB-09 3G8M TITLE SERINE HYDROXYMETHYLTRANSFERASE Y55F MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SERINE METHYLASE, SHMT; COMPND 5 EC: 2.1.2.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: B2551, ESCHERICHIA COLI GLYA, GLYA, JW2535; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: GS1993 RECA-; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBS::GLYA KEYWDS SHMT, E. COLI, Y55F, ONE-CARBON METABOLISM, PYRIDOXAL PHOSPHATE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.ANGELUCCI,A.ILARI REVDAT 5 06-SEP-23 3G8M 1 REMARK REVDAT 4 20-OCT-21 3G8M 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3G8M 1 VERSN REVDAT 2 26-JAN-10 3G8M 1 JRNL REVDAT 1 10-NOV-09 3G8M 0 JRNL AUTH M.VIVOLI,F.ANGELUCCI,A.ILARI,V.MOREA,S.ANGELACCIO, JRNL AUTH 2 M.L.DI SALVO,R.CONTESTABILE JRNL TITL ROLE OF A CONSERVED ACTIVE SITE CATION-PI INTERACTION IN JRNL TITL 2 ESCHERICHIA COLI SERINE HYDROXYMETHYLTRANSFERASE. JRNL REF BIOCHEMISTRY V. 48 12034 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19883126 JRNL DOI 10.1021/BI901568B REMARK 2 REMARK 2 RESOLUTION. 3.30 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 6356 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) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 319 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) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 464 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE SET COUNT : 21 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3185 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.17000 REMARK 3 B22 (A**2) : 3.17000 REMARK 3 B33 (A**2) : -6.34000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.669 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.579 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 80.811 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.896 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3283 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4451 ; 0.776 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 416 ; 3.404 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;34.637 ;24.755 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 540 ;14.009 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ; 3.504 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 482 ; 0.050 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2504 ; 0.001 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1278 ; 0.134 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2265 ; 0.284 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 49 ; 0.066 ; 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): 67 ; 0.095 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.031 ; 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): 2129 ; 0.022 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3296 ; 0.040 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1325 ; 0.051 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1155 ; 0.089 ; 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 : 5 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 1 A 35 REMARK 3 ORIGIN FOR THE GROUP (A): -22.4097 6.1658 16.7165 REMARK 3 T TENSOR REMARK 3 T11: 1.2579 T22: 0.1826 REMARK 3 T33: 0.6273 T12: 0.2292 REMARK 3 T13: -0.4782 T23: -0.0938 REMARK 3 L TENSOR REMARK 3 L11: 3.8791 L22: 0.9961 REMARK 3 L33: 6.6371 L12: 1.9566 REMARK 3 L13: 3.2216 L23: 1.4340 REMARK 3 S TENSOR REMARK 3 S11: 0.1948 S12: 0.8845 S13: -0.2424 REMARK 3 S21: 1.4185 S22: 0.0235 S23: -1.0547 REMARK 3 S31: -0.0965 S32: 1.3472 S33: -0.2183 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 36 A 118 REMARK 3 ORIGIN FOR THE GROUP (A): -19.6501 32.9703 12.4208 REMARK 3 T TENSOR REMARK 3 T11: -0.0197 T22: 0.4921 REMARK 3 T33: 0.0539 T12: -0.1507 REMARK 3 T13: 0.0350 T23: -0.0755 REMARK 3 L TENSOR REMARK 3 L11: 3.8989 L22: 5.5680 REMARK 3 L33: 5.8931 L12: 0.1299 REMARK 3 L13: 3.3945 L23: 0.6856 REMARK 3 S TENSOR REMARK 3 S11: -0.5531 S12: -0.1832 S13: 0.3297 REMARK 3 S21: 0.0163 S22: 0.4977 S23: -0.1381 REMARK 3 S31: -0.5933 S32: 1.0009 S33: 0.0554 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 119 A 192 REMARK 3 ORIGIN FOR THE GROUP (A): -40.4461 37.2310 -3.4941 REMARK 3 T TENSOR REMARK 3 T11: 1.0823 T22: 0.5058 REMARK 3 T33: 0.5964 T12: -0.2707 REMARK 3 T13: -0.4509 T23: 0.0896 REMARK 3 L TENSOR REMARK 3 L11: 7.6771 L22: 3.3280 REMARK 3 L33: 3.9475 L12: 1.6866 REMARK 3 L13: -2.1736 L23: -3.6167 REMARK 3 S TENSOR REMARK 3 S11: -1.0310 S12: 1.1453 S13: 0.2462 REMARK 3 S21: -1.1151 S22: 0.5599 S23: 1.1532 REMARK 3 S31: -0.5131 S32: 0.1581 S33: 0.4711 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 193 A 229 REMARK 3 ORIGIN FOR THE GROUP (A): -26.8622 34.2863 -2.4213 REMARK 3 T TENSOR REMARK 3 T11: 0.3954 T22: 0.4272 REMARK 3 T33: 0.1947 T12: -0.4208 REMARK 3 T13: -0.2505 T23: 0.0628 REMARK 3 L TENSOR REMARK 3 L11: 7.4761 L22: 2.1397 REMARK 3 L33: 9.7614 L12: -0.8817 REMARK 3 L13: -1.4987 L23: 2.1005 REMARK 3 S TENSOR REMARK 3 S11: -0.7102 S12: 0.6851 S13: 0.4166 REMARK 3 S21: -0.8269 S22: 0.0114 S23: 0.3089 REMARK 3 S31: -1.3929 S32: 1.2019 S33: 0.6988 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 230 A 417 REMARK 3 ORIGIN FOR THE GROUP (A): -30.3739 15.7579 -3.4097 REMARK 3 T TENSOR REMARK 3 T11: 0.1345 T22: 0.3851 REMARK 3 T33: 0.1509 T12: -0.0386 REMARK 3 T13: 0.0133 T23: -0.0411 REMARK 3 L TENSOR REMARK 3 L11: 1.8014 L22: 3.6336 REMARK 3 L33: 3.7176 L12: 1.8546 REMARK 3 L13: 1.9645 L23: 2.9245 REMARK 3 S TENSOR REMARK 3 S11: -0.1692 S12: 0.3231 S13: -0.0218 REMARK 3 S21: -0.2893 S22: 0.3048 S23: 0.1120 REMARK 3 S31: -0.1586 S32: 0.4899 S33: -0.1356 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 3G8M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97623 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6600 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1DFO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES (N-(2 REMARK 280 -HYDROXYLETHYL)PIPERAZINE-N -2 ETHANSULFONIC ACID) PH 7.5, 1.4M REMARK 280 SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 34.46450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 56.29500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 56.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.23225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 56.29500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 56.29500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.69675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 56.29500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.29500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.23225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 56.29500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.29500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.69675 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 34.46450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 34.46450 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 308 CG CD CE NZ 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 GLU A 5 -76.40 -136.43 REMARK 500 MET A 6 62.18 31.16 REMARK 500 ASP A 10 -11.29 -153.58 REMARK 500 TYR A 11 -61.44 -109.60 REMARK 500 SER A 35 18.39 58.05 REMARK 500 HIS A 123 69.47 -119.05 REMARK 500 GLN A 161 -7.88 67.91 REMARK 500 LYS A 166 78.46 55.73 REMARK 500 TYR A 177 4.99 49.16 REMARK 500 HIS A 228 18.75 -151.99 REMARK 500 LYS A 229 -103.35 -118.89 REMARK 500 ALA A 232 81.24 51.25 REMARK 500 PRO A 258 53.57 -92.76 REMARK 500 ASN A 316 -103.16 -124.01 REMARK 500 THR A 359 -18.16 68.30 REMARK 500 SER A 360 33.65 34.69 REMARK 500 SER A 392 77.84 -102.68 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 PLP A 418 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DFO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE REMARK 900 HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE AND 5-FORMYL REMARK 900 TETRAHYDROFOLATE DBREF 3G8M A 1 417 UNP P0A825 GLYA_ECOLI 1 417 SEQADV 3G8M PHE A 55 UNP P0A825 TYR 55 ENGINEERED MUTATION SEQRES 1 A 417 MET LEU LYS ARG GLU MET ASN ILE ALA ASP TYR ASP ALA SEQRES 2 A 417 GLU LEU TRP GLN ALA MET GLU GLN GLU LYS VAL ARG GLN SEQRES 3 A 417 GLU GLU HIS ILE GLU LEU ILE ALA SER GLU ASN TYR THR SEQRES 4 A 417 SER PRO ARG VAL MET GLN ALA GLN GLY SER GLN LEU THR SEQRES 5 A 417 ASN LYS PHE ALA GLU GLY TYR PRO GLY LYS ARG TYR TYR SEQRES 6 A 417 GLY GLY CYS GLU TYR VAL ASP ILE VAL GLU GLN LEU ALA SEQRES 7 A 417 ILE ASP ARG ALA LYS GLU LEU PHE GLY ALA ASP TYR ALA SEQRES 8 A 417 ASN VAL GLN PRO HIS SER GLY SER GLN ALA ASN PHE ALA SEQRES 9 A 417 VAL TYR THR ALA LEU LEU GLU PRO GLY ASP THR VAL LEU SEQRES 10 A 417 GLY MET ASN LEU ALA HIS GLY GLY HIS LEU THR HIS GLY SEQRES 11 A 417 SER PRO VAL ASN PHE SER GLY LYS LEU TYR ASN ILE VAL SEQRES 12 A 417 PRO TYR GLY ILE ASP ALA THR GLY HIS ILE ASP TYR ALA SEQRES 13 A 417 ASP LEU GLU LYS GLN ALA LYS GLU HIS LYS PRO LYS MET SEQRES 14 A 417 ILE ILE GLY GLY PHE SER ALA TYR SER GLY VAL VAL ASP SEQRES 15 A 417 TRP ALA LYS MET ARG GLU ILE ALA ASP SER ILE GLY ALA SEQRES 16 A 417 TYR LEU PHE VAL ASP MET ALA HIS VAL ALA GLY LEU VAL SEQRES 17 A 417 ALA ALA GLY VAL TYR PRO ASN PRO VAL PRO HIS ALA HIS SEQRES 18 A 417 VAL VAL THR THR THR THR HIS LYS THR LEU ALA GLY PRO SEQRES 19 A 417 ARG GLY GLY LEU ILE LEU ALA LYS GLY GLY SER GLU GLU SEQRES 20 A 417 LEU TYR LYS LYS LEU ASN SER ALA VAL PHE PRO GLY GLY SEQRES 21 A 417 GLN GLY GLY PRO LEU MET HIS VAL ILE ALA GLY LYS ALA SEQRES 22 A 417 VAL ALA LEU LYS GLU ALA MET GLU PRO GLU PHE LYS THR SEQRES 23 A 417 TYR GLN GLN GLN VAL ALA LYS ASN ALA LYS ALA MET VAL SEQRES 24 A 417 GLU VAL PHE LEU GLU ARG GLY TYR LYS VAL VAL SER GLY SEQRES 25 A 417 GLY THR ASP ASN HIS LEU PHE LEU VAL ASP LEU VAL ASP SEQRES 26 A 417 LYS ASN LEU THR GLY LYS GLU ALA ASP ALA ALA LEU GLY SEQRES 27 A 417 ARG ALA ASN ILE THR VAL ASN LYS ASN SER VAL PRO ASN SEQRES 28 A 417 ASP PRO LYS SER PRO PHE VAL THR SER GLY ILE ARG VAL SEQRES 29 A 417 GLY THR PRO ALA ILE THR ARG ARG GLY PHE LYS GLU ALA SEQRES 30 A 417 GLU ALA LYS GLU LEU ALA GLY TRP MET CYS ASP VAL LEU SEQRES 31 A 417 ASP SER ILE ASN ASP GLU ALA VAL ILE GLU ARG ILE LYS SEQRES 32 A 417 GLY LYS VAL LEU ASP ILE CYS ALA ARG TYR PRO VAL TYR SEQRES 33 A 417 ALA HET PLP A 418 30 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 PLP C8 H10 N O6 P HELIX 1 1 ASP A 12 HIS A 29 1 18 HELIX 2 2 SER A 40 GLY A 48 1 9 HELIX 3 3 SER A 49 ASN A 53 5 5 HELIX 4 4 TYR A 70 GLY A 87 1 18 HELIX 5 5 SER A 97 LEU A 110 1 14 HELIX 6 6 ASN A 120 GLY A 124 5 5 HELIX 7 7 HIS A 126 GLY A 130 5 5 HELIX 8 8 ASN A 134 TYR A 140 1 7 HELIX 9 9 ASP A 154 LYS A 160 1 7 HELIX 10 10 ASP A 182 GLY A 194 1 13 HELIX 11 11 VAL A 204 GLY A 211 1 8 HELIX 12 12 PRO A 216 ALA A 220 5 5 HELIX 13 13 SER A 245 PHE A 257 1 13 HELIX 14 14 LEU A 265 MET A 280 1 16 HELIX 15 15 GLU A 281 ARG A 305 1 25 HELIX 16 16 THR A 329 ALA A 340 1 12 HELIX 17 17 THR A 366 GLY A 373 1 8 HELIX 18 18 LYS A 375 SER A 392 1 18 HELIX 19 19 ASP A 395 TYR A 413 1 19 SHEET 1 A 2 ILE A 30 GLU A 31 0 SHEET 2 A 2 ILE A 342 THR A 343 1 O THR A 343 N ILE A 30 SHEET 1 B 2 GLY A 58 TYR A 59 0 SHEET 2 B 2 LYS A 62 ARG A 63 -1 O LYS A 62 N TYR A 59 SHEET 1 C 7 TYR A 90 ASN A 92 0 SHEET 2 C 7 GLY A 237 ALA A 241 -1 O ILE A 239 N ASN A 92 SHEET 3 C 7 VAL A 222 THR A 226 -1 N VAL A 223 O LEU A 240 SHEET 4 C 7 TYR A 196 ASP A 200 1 N VAL A 199 O VAL A 222 SHEET 5 C 7 MET A 169 ILE A 171 1 N ILE A 170 O TYR A 196 SHEET 6 C 7 THR A 115 LEU A 117 1 N LEU A 117 O MET A 169 SHEET 7 C 7 ASN A 141 ILE A 142 1 O ASN A 141 N VAL A 116 SHEET 1 D 4 LYS A 308 VAL A 309 0 SHEET 2 D 4 LEU A 318 ASP A 322 -1 O ASP A 322 N LYS A 308 SHEET 3 D 4 GLY A 361 GLY A 365 -1 O ILE A 362 N VAL A 321 SHEET 4 D 4 ASN A 345 LYS A 346 -1 N ASN A 345 O ARG A 363 LINK NZ LYS A 229 C4AAPLP A 418 1555 1555 1.53 LINK NZ LYS A 229 C4ABPLP A 418 1555 1555 1.52 CISPEP 1 PHE A 257 PRO A 258 0 0.72 SITE 1 AC1 11 PHE A 55 GLU A 57 SER A 97 GLY A 98 SITE 2 AC1 11 SER A 99 HIS A 126 THR A 226 HIS A 228 SITE 3 AC1 11 LYS A 229 ARG A 235 GLY A 263 CRYST1 112.590 112.590 68.929 90.00 90.00 90.00 P 41 21 2 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 0.008882 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014508 0.00000