PDB Short entry for 2Q4R HEADER ISOMERASE 31-MAY-07 2Q4R TITLE ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF HUMAN TITLE 2 PHOSPHOMANNOMUTASE 2 (PMM2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOMANNOMUTASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PMM 2; COMPND 5 EC: 5.4.2.8; COMPND 6 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: PMM2, HS.459855; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834 P(RARE2); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVP16 KEYWDS ENSEMBLE REFINEMENT, REFINEMENT METHODOLOGY DEVELOPMENT, HS.459855, KEYWDS 2 HS.313504, BC008310, PHOSPHATASE, PFAM PF03332, HAD SUPERFAMILY, KEYWDS 3 JAECKEN DISEASE, CARBOHYDRATE-DEFICIENT GLYCOPROTEIN SYNDROME, KEYWDS 4 STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, PSI, CENTER FOR KEYWDS 5 EUKARYOTIC STRUCTURAL GENOMICS, CESG, ISOMERASE EXPDTA X-RAY DIFFRACTION NUMMDL 16 AUTHOR E.J.LEVIN,D.A.KONDRASHOV,G.E.WESENBERG,G.N.PHILLIPS JR.,CENTER FOR AUTHOR 2 EUKARYOTIC STRUCTURAL GENOMICS (CESG) REVDAT 6 15-NOV-23 2Q4R 1 REMARK REVDAT 5 30-AUG-23 2Q4R 1 REMARK SEQADV LINK REVDAT 4 10-AUG-11 2Q4R 1 REMARK REVDAT 3 24-FEB-09 2Q4R 1 VERSN REVDAT 2 02-OCT-07 2Q4R 1 JRNL REVDAT 1 19-JUN-07 2Q4R 0 JRNL AUTH E.J.LEVIN,D.A.KONDRASHOV,G.E.WESENBERG,G.N.PHILLIPS JRNL TITL ENSEMBLE REFINEMENT OF PROTEIN CRYSTAL STRUCTURES: JRNL TITL 2 VALIDATION AND APPLICATION. JRNL REF STRUCTURE V. 15 1040 2007 JRNL REFN ISSN 0969-2126 JRNL PMID 17850744 JRNL DOI 10.1016/J.STR.2007.06.019 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD USING AMPLITUDES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1443312.250 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 17513 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 SET) : 0.207 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 924 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.22 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2647 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 175 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1943 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 142 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.90 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.510 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.220 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.650 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 55.45 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : GLY_XPLOR_PAR.TXT REMARK 3 PARAMETER FILE 4 : EDO.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THIS PDB ENTRY IS A RE-REFINEMENT USING AN ENSEMBLE MODEL OF THE REMARK 3 PREVIOUSLY REMARK 3 DEPOSITED SINGLE-CONFORMER STRUCTURE 2AMY AND REMARK 3 THE FIRST DATA SET IN THE DEPOSITED STRUCTURE FACTOR FILE REMARK 3 FOR 2AMY ALONG WITH THE R-FREE SET DEFINED THEREIN. THE COORDINATES REMARK 3 WERE GENERATED BY AN AUTOMATED PROTOCOL FROM AN INITIAL MODEL REMARK 3 CONSISTING REMARK 3 OF 16 IDENTICAL COPIES OF THE PROTEIN AND NON-WATER REMARK 3 HETERO-ATOMS ASSIGNED FRACTIONAL OCCUPANCIES ADDING UP TO ONE, AND REMARK 3 A REMARK 3 SINGLE COPY OF THE SOLVENT MOLECULES. REFINEMENT WAS CARRIED OUT REMARK 3 WITH REMARK 3 ALL THE CONFORMERS PRESENT SIMULTANEOUSLY AND WITH THE POTENTIAL REMARK 3 ENERGY REMARK 3 TERMS CORRESPONDING TO INTERACTIONS BETWEEN THE DIFFERENT REMARK 3 CONFORMERS REMARK 3 EXCLUDED. THE HELIX AND SHEET RECORDS WERE CALCULATED USING REMARK 3 COORDINATES REMARK 3 FROM THE FIRST CONFORMER ONLY. THE STRUCTURE VISUALIZATION PROGRAM REMARK 3 PYMOL IS WELL-SUITED FOR DIRECTLY VIEWING THE ENSEMBLE MODEL REMARK 3 PRESENTED IN THIS PDB FILE. REMARK 4 REMARK 4 2Q4R COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043147. 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) : M 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RE-REFINEMENT USING REMARK 200 ENSEMBLE MODEL REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: PDB ENTRY 2AMY REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 2AMY. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 66.76667 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 33.38333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.38333 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 66.76667 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 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 449 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 1 SER A 1 REMARK 465 1 ALA A 2 REMARK 465 1 ALA A 3 REMARK 465 1 PRO A 213 REMARK 465 1 GLY A 214 REMARK 465 1 GLY A 215 REMARK 465 2 SER A 1 REMARK 465 2 ALA A 2 REMARK 465 2 ALA A 3 REMARK 465 2 PRO A 213 REMARK 465 2 GLY A 214 REMARK 465 2 GLY A 215 REMARK 465 3 SER A 1 REMARK 465 3 ALA A 2 REMARK 465 3 ALA A 3 REMARK 465 3 PRO A 213 REMARK 465 3 GLY A 214 REMARK 465 3 GLY A 215 REMARK 465 4 SER A 1 REMARK 465 4 ALA A 2 REMARK 465 4 ALA A 3 REMARK 465 4 PRO A 213 REMARK 465 4 GLY A 214 REMARK 465 4 GLY A 215 REMARK 465 5 SER A 1 REMARK 465 5 ALA A 2 REMARK 465 5 ALA A 3 REMARK 465 5 PRO A 213 REMARK 465 5 GLY A 214 REMARK 465 5 GLY A 215 REMARK 465 6 SER A 1 REMARK 465 6 ALA A 2 REMARK 465 6 ALA A 3 REMARK 465 6 PRO A 213 REMARK 465 6 GLY A 214 REMARK 465 6 GLY A 215 REMARK 465 7 SER A 1 REMARK 465 7 ALA A 2 REMARK 465 7 ALA A 3 REMARK 465 7 PRO A 213 REMARK 465 7 GLY A 214 REMARK 465 7 GLY A 215 REMARK 465 8 SER A 1 REMARK 465 8 ALA A 2 REMARK 465 8 ALA A 3 REMARK 465 8 PRO A 213 REMARK 465 8 GLY A 214 REMARK 465 8 GLY A 215 REMARK 465 9 SER A 1 REMARK 465 9 ALA A 2 REMARK 465 9 ALA A 3 REMARK 465 9 PRO A 213 REMARK 465 9 GLY A 214 REMARK 465 9 GLY A 215 REMARK 465 10 SER A 1 REMARK 465 10 ALA A 2 REMARK 465 10 ALA A 3 REMARK 465 10 PRO A 213 REMARK 465 10 GLY A 214 REMARK 465 10 GLY A 215 REMARK 465 11 SER A 1 REMARK 465 11 ALA A 2 REMARK 465 11 ALA A 3 REMARK 465 11 PRO A 213 REMARK 465 11 GLY A 214 REMARK 465 11 GLY A 215 REMARK 465 12 SER A 1 REMARK 465 12 ALA A 2 REMARK 465 12 ALA A 3 REMARK 465 12 PRO A 213 REMARK 465 12 GLY A 214 REMARK 465 12 GLY A 215 REMARK 465 13 SER A 1 REMARK 465 13 ALA A 2 REMARK 465 13 ALA A 3 REMARK 465 13 PRO A 213 REMARK 465 13 GLY A 214 REMARK 465 13 GLY A 215 REMARK 465 14 SER A 1 REMARK 465 14 ALA A 2 REMARK 465 14 ALA A 3 REMARK 465 14 PRO A 213 REMARK 465 14 GLY A 214 REMARK 465 14 GLY A 215 REMARK 465 15 SER A 1 REMARK 465 15 ALA A 2 REMARK 465 15 ALA A 3 REMARK 465 15 PRO A 213 REMARK 465 15 GLY A 214 REMARK 465 15 GLY A 215 REMARK 465 16 SER A 1 REMARK 465 16 ALA A 2 REMARK 465 16 ALA A 3 REMARK 465 16 PRO A 213 REMARK 465 16 GLY A 214 REMARK 465 16 GLY A 215 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 1 VAL A 13 -83.95 -73.53 REMARK 500 1 LEU A 81 99.73 -61.96 REMARK 500 1 GLN A 85 129.13 -173.81 REMARK 500 1 LYS A 109 51.75 -104.33 REMARK 500 1 ARG A 116 -93.58 -126.52 REMARK 500 1 MSE A 126 137.45 -174.11 REMARK 500 1 VAL A 129 -155.87 -87.26 REMARK 500 1 SER A 130 114.70 143.90 REMARK 500 1 ARG A 134 -26.65 -171.32 REMARK 500 1 SER A 137 -165.06 -71.61 REMARK 500 1 SER A 173 116.06 -165.59 REMARK 500 1 TRP A 187 47.69 -79.20 REMARK 500 1 ASP A 188 -162.71 -112.97 REMARK 500 1 ASP A 217 116.54 -173.22 REMARK 500 1 ALA A 233 175.12 177.32 REMARK 500 2 VAL A 13 -83.82 -76.73 REMARK 500 2 LEU A 82 -62.13 -106.11 REMARK 500 2 GLU A 93 -75.51 -35.15 REMARK 500 2 LYS A 109 50.46 -95.89 REMARK 500 2 ARG A 116 -99.68 -127.35 REMARK 500 2 ILE A 153 -74.32 -62.45 REMARK 500 2 TRP A 187 45.50 -101.35 REMARK 500 2 ASP A 188 -160.03 -107.13 REMARK 500 2 LYS A 210 28.93 -170.88 REMARK 500 2 ASP A 223 113.07 -37.36 REMARK 500 2 PRO A 224 -15.48 -44.73 REMARK 500 3 VAL A 13 -91.42 -80.86 REMARK 500 3 ARG A 21 22.26 46.52 REMARK 500 3 ARG A 36 9.81 -61.74 REMARK 500 3 GLN A 37 -74.18 -78.31 REMARK 500 3 ASN A 71 -5.75 60.98 REMARK 500 3 LEU A 82 -60.28 -108.72 REMARK 500 3 ARG A 116 -109.12 -118.90 REMARK 500 3 CYS A 192 8.84 -62.28 REMARK 500 3 ASP A 217 129.51 173.29 REMARK 500 3 ALA A 233 175.20 173.10 REMARK 500 3 LEU A 244 -14.91 -147.10 REMARK 500 3 PHE A 245 -135.43 -135.85 REMARK 500 4 PRO A 6 91.59 -37.57 REMARK 500 4 ALA A 7 -145.92 -114.11 REMARK 500 4 LEU A 8 107.22 -172.95 REMARK 500 4 ASP A 12 -156.70 -79.58 REMARK 500 4 VAL A 13 -82.51 -124.67 REMARK 500 4 PRO A 20 153.34 -47.19 REMARK 500 4 ARG A 21 43.34 37.97 REMARK 500 4 ARG A 116 -99.81 -131.05 REMARK 500 4 THR A 118 60.01 69.45 REMARK 500 4 SER A 135 -14.24 -45.62 REMARK 500 4 TRP A 187 36.13 -79.09 REMARK 500 4 ASP A 188 -165.47 -103.30 REMARK 500 REMARK 500 THIS ENTRY HAS 264 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1 GLY A 400 REMARK 610 1 GLY A 401 REMARK 610 1 GLY A 402 REMARK 610 2 GLY A 400 REMARK 610 2 GLY A 401 REMARK 610 2 GLY A 402 REMARK 610 3 GLY A 400 REMARK 610 3 GLY A 401 REMARK 610 3 GLY A 402 REMARK 610 4 GLY A 400 REMARK 610 4 GLY A 401 REMARK 610 4 GLY A 402 REMARK 610 5 GLY A 400 REMARK 610 5 GLY A 401 REMARK 610 5 GLY A 402 REMARK 610 6 GLY A 400 REMARK 610 6 GLY A 401 REMARK 610 6 GLY A 402 REMARK 610 7 GLY A 400 REMARK 610 7 GLY A 401 REMARK 610 7 GLY A 402 REMARK 610 8 GLY A 400 REMARK 610 8 GLY A 401 REMARK 610 8 GLY A 402 REMARK 610 9 GLY A 400 REMARK 610 9 GLY A 401 REMARK 610 9 GLY A 402 REMARK 610 10 GLY A 400 REMARK 610 10 GLY A 401 REMARK 610 10 GLY A 402 REMARK 610 11 GLY A 400 REMARK 610 11 GLY A 401 REMARK 610 11 GLY A 402 REMARK 610 12 GLY A 400 REMARK 610 12 GLY A 401 REMARK 610 12 GLY A 402 REMARK 610 13 GLY A 400 REMARK 610 13 GLY A 401 REMARK 610 13 GLY A 402 REMARK 610 14 GLY A 400 REMARK 610 14 GLY A 401 REMARK 610 14 GLY A 402 REMARK 610 15 GLY A 400 REMARK 610 15 GLY A 401 REMARK 610 15 GLY A 402 REMARK 610 16 GLY A 400 REMARK 610 16 GLY A 401 REMARK 610 16 GLY A 402 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLY A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLY A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLY A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GO.36653 RELATED DB: TARGETDB REMARK 900 RELATED ID: 2AMY RELATED DB: PDB REMARK 900 ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET. DBREF 2Q4R A 2 246 UNP O15305 PMM2_HUMAN 2 246 SEQADV 2Q4R SER A 1 UNP O15305 EXPRESSION TAG SEQADV 2Q4R MSE A 28 UNP O15305 MET 28 MODIFIED RESIDUE SEQADV 2Q4R MSE A 126 UNP O15305 MET 126 MODIFIED RESIDUE SEQADV 2Q4R MSE A 212 UNP O15305 MET 212 MODIFIED RESIDUE SEQADV 2Q4R MSE A 227 UNP O15305 MET 227 MODIFIED RESIDUE SEQRES 1 A 246 SER ALA ALA PRO GLY PRO ALA LEU CYS LEU PHE ASP VAL SEQRES 2 A 246 ASP GLY THR LEU THR ALA PRO ARG GLN LYS ILE THR LYS SEQRES 3 A 246 GLU MSE ASP ASP PHE LEU GLN LYS LEU ARG GLN LYS ILE SEQRES 4 A 246 LYS ILE GLY VAL VAL GLY GLY SER ASP PHE GLU LYS VAL SEQRES 5 A 246 GLN GLU GLN LEU GLY ASN ASP VAL VAL GLU LYS TYR ASP SEQRES 6 A 246 TYR VAL PHE PRO GLU ASN GLY LEU VAL ALA TYR LYS ASP SEQRES 7 A 246 GLY LYS LEU LEU CYS ARG GLN ASN ILE GLN SER HIS LEU SEQRES 8 A 246 GLY GLU ALA LEU ILE GLN ASP LEU ILE ASN TYR CYS LEU SEQRES 9 A 246 SER TYR ILE ALA LYS ILE LYS LEU PRO LYS LYS ARG GLY SEQRES 10 A 246 THR PHE ILE GLU PHE ARG ASN GLY MSE LEU ASN VAL SER SEQRES 11 A 246 PRO ILE GLY ARG SER CYS SER GLN GLU GLU ARG ILE GLU SEQRES 12 A 246 PHE TYR GLU LEU ASP LYS LYS GLU ASN ILE ARG GLN LYS SEQRES 13 A 246 PHE VAL ALA ASP LEU ARG LYS GLU PHE ALA GLY LYS GLY SEQRES 14 A 246 LEU THR PHE SER ILE GLY GLY GLN ILE SER PHE ASP VAL SEQRES 15 A 246 PHE PRO ASP GLY TRP ASP LYS ARG TYR CYS LEU ARG HIS SEQRES 16 A 246 VAL GLU ASN ASP GLY TYR LYS THR ILE TYR PHE PHE GLY SEQRES 17 A 246 ASP LYS THR MSE PRO GLY GLY ASN ASP HIS GLU ILE PHE SEQRES 18 A 246 THR ASP PRO ARG THR MSE GLY TYR SER VAL THR ALA PRO SEQRES 19 A 246 GLU ASP THR ARG ARG ILE CYS GLU LEU LEU PHE SER MODRES 2Q4R MSE A 28 MET SELENOMETHIONINE MODRES 2Q4R MSE A 126 MET SELENOMETHIONINE MODRES 2Q4R MSE A 212 MET SELENOMETHIONINE MODRES 2Q4R MSE A 227 MET SELENOMETHIONINE HET MSE A 28 8 HET MSE A 126 8 HET MSE A 212 8 HET MSE A 227 8 HET EDO A 300 4 HET GLY A 400 4 HET GLY A 401 4 HET GLY A 402 4 HETNAM MSE SELENOMETHIONINE HETNAM EDO 1,2-ETHANEDIOL HETNAM GLY GLYCINE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 EDO C2 H6 O2 FORMUL 3 GLY 3(C2 H5 N O2) FORMUL 6 HOH *142(H2 O) HELIX 1 1 THR A 25 GLN A 37 1 13 HELIX 2 2 ASP A 48 GLY A 57 1 10 HELIX 3 3 ASP A 59 TYR A 64 1 6 HELIX 4 4 PRO A 69 LEU A 73 5 5 HELIX 5 5 ASN A 86 GLY A 92 1 7 HELIX 6 6 GLY A 92 ALA A 108 1 17 HELIX 7 7 SER A 137 ASN A 152 1 16 HELIX 8 8 ASN A 152 PHE A 165 1 14 HELIX 9 9 ASP A 188 VAL A 196 5 9 HELIX 10 10 HIS A 218 ASP A 223 1 6 HELIX 11 11 ALA A 233 PHE A 245 1 13 SHEET 1 A 7 LYS A 80 CYS A 83 0 SHEET 2 A 7 ALA A 75 LYS A 77 -1 N ALA A 75 O LEU A 82 SHEET 3 A 7 TYR A 66 PHE A 68 -1 N VAL A 67 O TYR A 76 SHEET 4 A 7 LYS A 40 VAL A 44 1 N VAL A 43 O PHE A 68 SHEET 5 A 7 ALA A 7 ASP A 12 1 N PHE A 11 O VAL A 44 SHEET 6 A 7 THR A 203 GLY A 208 1 O PHE A 207 N ASP A 12 SHEET 7 A 7 THR A 226 SER A 230 1 O MSE A 227 N ILE A 204 SHEET 1 B 4 GLU A 121 ARG A 123 0 SHEET 2 B 4 MSE A 126 ASN A 128 -1 O ASN A 128 N GLU A 121 SHEET 3 B 4 PHE A 180 PRO A 184 -1 O VAL A 182 N LEU A 127 SHEET 4 B 4 LEU A 170 ILE A 174 -1 N THR A 171 O PHE A 183 LINK C GLU A 27 N MSE A 28 1555 1555 1.33 LINK C MSE A 28 N ASP A 29 1555 1555 1.33 LINK C GLY A 125 N MSE A 126 1555 1555 1.33 LINK C MSE A 126 N LEU A 127 1555 1555 1.33 LINK C THR A 211 N MSE A 212 1555 1555 1.33 LINK C THR A 226 N MSE A 227 1555 1555 1.33 LINK C MSE A 227 N GLY A 228 1555 1555 1.33 SITE 1 AC1 4 TYR A 106 LYS A 109 LYS A 156 GLY A 402 SITE 1 AC2 5 ARG A 21 TYR A 201 LYS A 202 ARG A 225 SITE 2 AC2 5 HOH A 480 SITE 1 AC3 5 PHE A 221 THR A 222 ASP A 223 THR A 226 SITE 2 AC3 5 GLY A 228 SITE 1 AC4 4 SER A 105 TYR A 106 LYS A 109 EDO A 300 CRYST1 70.622 70.622 100.150 90.00 90.00 120.00 P 32 2 1 6 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 0.014160 0.008175 0.000000 0.00000 SCALE2 0.000000 0.016350 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009985 0.00000