HEADER TRANSFERASE 17-MAR-14 4PVF TITLE CRYSTAL STRUCTURE OF HOMO SAPIENS HOLO SERINE HYDROXYMETHYLTRANSFERASE TITLE 2 2 (MITOCHONDRIAL) (SHMT2), ISOFORM 3, TRANSCRIPT VARIANT 5, 483 AA, TITLE 3 AT 2.6 ANG. RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SHMT, GLYCINE HYDROXYMETHYLTRANSFERASE, SERINE METHYLASE; COMPND 5 EC: 2.1.2.1; 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: SHMT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS HYDROXYMETHYLTRANSFERASE, AAT-LIKE FOLD, ONE CARBON METABOLISM, KEYWDS 2 TRANSFERASE, 5-FORMYL-THF, METHYLASE, MITOCHONDRIAL EXPDTA X-RAY DIFFRACTION AUTHOR G.GIARDINA,P.BRUNOTTI,A.FIASCARELLI,R.CONTESTABILE,F.CUTRUZZOLA REVDAT 6 06-DEC-23 4PVF 1 REMARK REVDAT 5 20-SEP-23 4PVF 1 REMARK LINK REVDAT 4 22-NOV-17 4PVF 1 REMARK REVDAT 3 22-APR-15 4PVF 1 JRNL REVDAT 2 25-FEB-15 4PVF 1 JRNL REVDAT 1 28-JAN-15 4PVF 0 JRNL AUTH G.GIARDINA,P.BRUNOTTI,A.FIASCARELLI,A.CICALINI,M.G.COSTA, JRNL AUTH 2 A.M.BUCKLE,M.L.DI SALVO,A.GIORGI,M.MARANI,A.PAONE,S.RINALDO, JRNL AUTH 3 A.PAIARDINI,R.CONTESTABILE,F.CUTRUZZOLA JRNL TITL HOW PYRIDOXAL 5'-PHOSPHATE DIFFERENTIALLY REGULATES HUMAN JRNL TITL 2 CYTOSOLIC AND MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASE JRNL TITL 3 OLIGOMERIC STATE. JRNL REF FEBS J. V. 282 1225 2015 JRNL REFN ISSN 1742-464X JRNL PMID 25619277 JRNL DOI 10.1111/FEBS.13211 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 138.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 49926 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2531 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3442 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 194 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7073 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.46000 REMARK 3 B22 (A**2) : 0.46000 REMARK 3 B33 (A**2) : -1.49000 REMARK 3 B12 (A**2) : 0.23000 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): 0.341 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.252 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.200 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7244 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6970 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9797 ; 1.747 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15992 ; 1.141 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 900 ; 6.516 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 336 ;36.152 ;23.036 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1222 ;18.639 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 69 ;21.794 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1077 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8218 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1697 ; 0.004 ; 0.020 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): 3603 ; 2.737 ; 3.314 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3602 ; 2.737 ; 3.313 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4496 ; 4.329 ; 4.959 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 22 483 B 22 483 27719 0.080 0.050 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4PVF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-13 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) : 0.9798 REMARK 200 MONOCHROMATOR : S111 REMARK 200 OPTICS : SAGITALLY BENDED SI111-CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 0.1.29, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49990 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 138.964 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 15.40 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) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: PDB ENTRY 3OU5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE PH7.5, REMARK 280 5%GLYCEROL, 12-16% PEG 3350, 0.2M KF, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 140.97400 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 70.48700 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 105.73050 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.24350 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 176.21750 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 140.97400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 70.48700 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 35.24350 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 105.73050 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 176.21750 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 23050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.500000 -0.866025 0.000000 80.23100 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 138.96417 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 35.24350 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 ALA A 2 REMARK 465 ILE A 3 REMARK 465 ARG A 4 REMARK 465 ALA A 5 REMARK 465 GLN A 6 REMARK 465 HIS A 7 REMARK 465 SER A 8 REMARK 465 ASN A 9 REMARK 465 ALA A 10 REMARK 465 ALA A 11 REMARK 465 GLN A 12 REMARK 465 THR A 13 REMARK 465 GLN A 14 REMARK 465 THR A 15 REMARK 465 GLY A 16 REMARK 465 GLU A 17 REMARK 465 ALA A 18 REMARK 465 ASN A 19 REMARK 465 ARG A 20 REMARK 465 GLY A 21 REMARK 465 VAL A 278 REMARK 465 ASP A 279 REMARK 465 PRO A 280 REMARK 465 LYS A 281 REMARK 465 THR A 282 REMARK 465 GLY A 283 REMARK 465 ARG A 284 REMARK 465 GLU A 285 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ILE B 3 REMARK 465 ARG B 4 REMARK 465 ALA B 5 REMARK 465 GLN B 6 REMARK 465 HIS B 7 REMARK 465 SER B 8 REMARK 465 ASN B 9 REMARK 465 ALA B 10 REMARK 465 ALA B 11 REMARK 465 GLN B 12 REMARK 465 THR B 13 REMARK 465 GLN B 14 REMARK 465 THR B 15 REMARK 465 GLY B 16 REMARK 465 GLU B 17 REMARK 465 ALA B 18 REMARK 465 ASN B 19 REMARK 465 ARG B 20 REMARK 465 GLY B 21 REMARK 465 VAL B 278 REMARK 465 ASP B 279 REMARK 465 PRO B 280 REMARK 465 LYS B 281 REMARK 465 THR B 282 REMARK 465 GLY B 283 REMARK 465 ARG B 284 REMARK 465 GLU B 285 REMARK 465 PRO B 392 REMARK 465 GLY B 393 REMARK 465 ASP B 394 REMARK 465 ARG B 395 REMARK 465 SER B 396 REMARK 465 ALA B 397 REMARK 465 ILE B 398 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 OH TYR A 85 O1 GOL B 501 2.07 REMARK 500 OH TYR B 85 O2 GOL A 501 2.13 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 ARG A 48 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 161 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASN A 387 CB - CA - C ANGL. DEV. = -14.2 DEGREES REMARK 500 CYS A 391 CB - CA - C ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG B 265 CG - CD - NE ANGL. DEV. = -13.4 DEGREES REMARK 500 ASN B 387 CB - CA - C ANGL. DEV. = -14.0 DEGREES REMARK 500 ASP B 425 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP B 425 CB - CG - OD2 ANGL. DEV. = -5.5 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 LYS A 82 56.79 -143.61 REMARK 500 SER A 121 -169.31 -160.98 REMARK 500 HIS A 258 -143.44 -88.93 REMARK 500 LLP A 259 -134.79 50.17 REMARK 500 SER A 266 -174.77 -172.61 REMARK 500 ASN A 358 -141.56 -144.38 REMARK 500 ALA A 397 -58.14 104.21 REMARK 500 ALA A 442 -72.68 -99.37 REMARK 500 LYS B 82 59.84 -144.41 REMARK 500 SER B 121 -168.44 -161.95 REMARK 500 HIS B 258 -146.00 -89.95 REMARK 500 LLP B 259 -136.34 53.31 REMARK 500 SER B 266 -174.53 -171.69 REMARK 500 ASN B 358 -141.82 -144.44 REMARK 500 ALA B 442 -78.70 -100.97 REMARK 500 LYS B 453 -68.49 -109.94 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 GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 501 DBREF 4PVF A 1 483 UNP P34897 GLYM_HUMAN 22 504 DBREF 4PVF B 1 483 UNP P34897 GLYM_HUMAN 22 504 SEQRES 1 A 483 MET ALA ILE ARG ALA GLN HIS SER ASN ALA ALA GLN THR SEQRES 2 A 483 GLN THR GLY GLU ALA ASN ARG GLY TRP THR GLY GLN GLU SEQRES 3 A 483 SER LEU SER ASP SER ASP PRO GLU MET TRP GLU LEU LEU SEQRES 4 A 483 GLN ARG GLU LYS ASP ARG GLN CYS ARG GLY LEU GLU LEU SEQRES 5 A 483 ILE ALA SER GLU ASN PHE CYS SER ARG ALA ALA LEU GLU SEQRES 6 A 483 ALA LEU GLY SER CYS LEU ASN ASN LYS TYR SER GLU GLY SEQRES 7 A 483 TYR PRO GLY LYS ARG TYR TYR GLY GLY ALA GLU VAL VAL SEQRES 8 A 483 ASP GLU ILE GLU LEU LEU CYS GLN ARG ARG ALA LEU GLU SEQRES 9 A 483 ALA PHE ASP LEU ASP PRO ALA GLN TRP GLY VAL ASN VAL SEQRES 10 A 483 GLN PRO TYR SER GLY SER PRO ALA ASN LEU ALA VAL TYR SEQRES 11 A 483 THR ALA LEU LEU GLN PRO HIS ASP ARG ILE MET GLY LEU SEQRES 12 A 483 ASP LEU PRO ASP GLY GLY HIS LEU THR HIS GLY TYR MET SEQRES 13 A 483 SER ASP VAL LYS ARG ILE SER ALA THR SER ILE PHE PHE SEQRES 14 A 483 GLU SER MET PRO TYR LYS LEU ASN PRO LYS THR GLY LEU SEQRES 15 A 483 ILE ASP TYR ASN GLN LEU ALA LEU THR ALA ARG LEU PHE SEQRES 16 A 483 ARG PRO ARG LEU ILE ILE ALA GLY THR SER ALA TYR ALA SEQRES 17 A 483 ARG LEU ILE ASP TYR ALA ARG MET ARG GLU VAL CYS ASP SEQRES 18 A 483 GLU VAL LYS ALA HIS LEU LEU ALA ASP MET ALA HIS ILE SEQRES 19 A 483 SER GLY LEU VAL ALA ALA LYS VAL ILE PRO SER PRO PHE SEQRES 20 A 483 LYS HIS ALA ASP ILE VAL THR THR THR THR HIS LLP THR SEQRES 21 A 483 LEU ARG GLY ALA ARG SER GLY LEU ILE PHE TYR ARG LYS SEQRES 22 A 483 GLY VAL LYS ALA VAL ASP PRO LYS THR GLY ARG GLU ILE SEQRES 23 A 483 PRO TYR THR PHE GLU ASP ARG ILE ASN PHE ALA VAL PHE SEQRES 24 A 483 PRO SER LEU GLN GLY GLY PRO HIS ASN HIS ALA ILE ALA SEQRES 25 A 483 ALA VAL ALA VAL ALA LEU LYS GLN ALA CYS THR PRO MET SEQRES 26 A 483 PHE ARG GLU TYR SER LEU GLN VAL LEU LYS ASN ALA ARG SEQRES 27 A 483 ALA MET ALA ASP ALA LEU LEU GLU ARG GLY TYR SER LEU SEQRES 28 A 483 VAL SER GLY GLY THR ASP ASN HIS LEU VAL LEU VAL ASP SEQRES 29 A 483 LEU ARG PRO LYS GLY LEU ASP GLY ALA ARG ALA GLU ARG SEQRES 30 A 483 VAL LEU GLU LEU VAL SER ILE THR ALA ASN LYS ASN THR SEQRES 31 A 483 CYS PRO GLY ASP ARG SER ALA ILE THR PRO GLY GLY LEU SEQRES 32 A 483 ARG LEU GLY ALA PRO ALA LEU THR SER ARG GLN PHE ARG SEQRES 33 A 483 GLU ASP ASP PHE ARG ARG VAL VAL ASP PHE ILE ASP GLU SEQRES 34 A 483 GLY VAL ASN ILE GLY LEU GLU VAL LYS SER LYS THR ALA SEQRES 35 A 483 LYS LEU GLN ASP PHE LYS SER PHE LEU LEU LYS ASP SER SEQRES 36 A 483 GLU THR SER GLN ARG LEU ALA ASN LEU ARG GLN ARG VAL SEQRES 37 A 483 GLU GLN PHE ALA ARG ALA PHE PRO MET PRO GLY PHE ASP SEQRES 38 A 483 GLU HIS SEQRES 1 B 483 MET ALA ILE ARG ALA GLN HIS SER ASN ALA ALA GLN THR SEQRES 2 B 483 GLN THR GLY GLU ALA ASN ARG GLY TRP THR GLY GLN GLU SEQRES 3 B 483 SER LEU SER ASP SER ASP PRO GLU MET TRP GLU LEU LEU SEQRES 4 B 483 GLN ARG GLU LYS ASP ARG GLN CYS ARG GLY LEU GLU LEU SEQRES 5 B 483 ILE ALA SER GLU ASN PHE CYS SER ARG ALA ALA LEU GLU SEQRES 6 B 483 ALA LEU GLY SER CYS LEU ASN ASN LYS TYR SER GLU GLY SEQRES 7 B 483 TYR PRO GLY LYS ARG TYR TYR GLY GLY ALA GLU VAL VAL SEQRES 8 B 483 ASP GLU ILE GLU LEU LEU CYS GLN ARG ARG ALA LEU GLU SEQRES 9 B 483 ALA PHE ASP LEU ASP PRO ALA GLN TRP GLY VAL ASN VAL SEQRES 10 B 483 GLN PRO TYR SER GLY SER PRO ALA ASN LEU ALA VAL TYR SEQRES 11 B 483 THR ALA LEU LEU GLN PRO HIS ASP ARG ILE MET GLY LEU SEQRES 12 B 483 ASP LEU PRO ASP GLY GLY HIS LEU THR HIS GLY TYR MET SEQRES 13 B 483 SER ASP VAL LYS ARG ILE SER ALA THR SER ILE PHE PHE SEQRES 14 B 483 GLU SER MET PRO TYR LYS LEU ASN PRO LYS THR GLY LEU SEQRES 15 B 483 ILE ASP TYR ASN GLN LEU ALA LEU THR ALA ARG LEU PHE SEQRES 16 B 483 ARG PRO ARG LEU ILE ILE ALA GLY THR SER ALA TYR ALA SEQRES 17 B 483 ARG LEU ILE ASP TYR ALA ARG MET ARG GLU VAL CYS ASP SEQRES 18 B 483 GLU VAL LYS ALA HIS LEU LEU ALA ASP MET ALA HIS ILE SEQRES 19 B 483 SER GLY LEU VAL ALA ALA LYS VAL ILE PRO SER PRO PHE SEQRES 20 B 483 LYS HIS ALA ASP ILE VAL THR THR THR THR HIS LLP THR SEQRES 21 B 483 LEU ARG GLY ALA ARG SER GLY LEU ILE PHE TYR ARG LYS SEQRES 22 B 483 GLY VAL LYS ALA VAL ASP PRO LYS THR GLY ARG GLU ILE SEQRES 23 B 483 PRO TYR THR PHE GLU ASP ARG ILE ASN PHE ALA VAL PHE SEQRES 24 B 483 PRO SER LEU GLN GLY GLY PRO HIS ASN HIS ALA ILE ALA SEQRES 25 B 483 ALA VAL ALA VAL ALA LEU LYS GLN ALA CYS THR PRO MET SEQRES 26 B 483 PHE ARG GLU TYR SER LEU GLN VAL LEU LYS ASN ALA ARG SEQRES 27 B 483 ALA MET ALA ASP ALA LEU LEU GLU ARG GLY TYR SER LEU SEQRES 28 B 483 VAL SER GLY GLY THR ASP ASN HIS LEU VAL LEU VAL ASP SEQRES 29 B 483 LEU ARG PRO LYS GLY LEU ASP GLY ALA ARG ALA GLU ARG SEQRES 30 B 483 VAL LEU GLU LEU VAL SER ILE THR ALA ASN LYS ASN THR SEQRES 31 B 483 CYS PRO GLY ASP ARG SER ALA ILE THR PRO GLY GLY LEU SEQRES 32 B 483 ARG LEU GLY ALA PRO ALA LEU THR SER ARG GLN PHE ARG SEQRES 33 B 483 GLU ASP ASP PHE ARG ARG VAL VAL ASP PHE ILE ASP GLU SEQRES 34 B 483 GLY VAL ASN ILE GLY LEU GLU VAL LYS SER LYS THR ALA SEQRES 35 B 483 LYS LEU GLN ASP PHE LYS SER PHE LEU LEU LYS ASP SER SEQRES 36 B 483 GLU THR SER GLN ARG LEU ALA ASN LEU ARG GLN ARG VAL SEQRES 37 B 483 GLU GLN PHE ALA ARG ALA PHE PRO MET PRO GLY PHE ASP SEQRES 38 B 483 GLU HIS MODRES 4PVF LLP A 259 LYS MODRES 4PVF LLP B 259 LYS HET LLP A 259 24 HET LLP B 259 24 HET GOL A 501 6 HET PEG A 502 7 HET GOL B 501 6 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 GOL 2(C3 H8 O3) FORMUL 4 PEG C4 H10 O3 FORMUL 6 HOH *126(H2 O) HELIX 1 1 SER A 27 ASP A 32 1 6 HELIX 2 2 ASP A 32 GLY A 49 1 18 HELIX 3 3 SER A 60 GLY A 68 1 9 HELIX 4 4 SER A 69 LYS A 74 5 6 HELIX 5 5 ALA A 88 PHE A 106 1 19 HELIX 6 6 SER A 121 LEU A 134 1 14 HELIX 7 7 LEU A 145 GLY A 148 5 4 HELIX 8 8 HIS A 150 GLY A 154 5 5 HELIX 9 9 ALA A 164 PHE A 169 1 6 HELIX 10 10 ASP A 184 ARG A 196 1 13 HELIX 11 11 ASP A 212 LYS A 224 1 13 HELIX 12 12 ILE A 234 ALA A 240 1 7 HELIX 13 13 SER A 245 HIS A 249 5 5 HELIX 14 14 HIS A 258 ARG A 262 5 5 HELIX 15 15 THR A 289 PHE A 299 1 11 HELIX 16 16 HIS A 307 THR A 323 1 17 HELIX 17 17 THR A 323 GLU A 346 1 24 HELIX 18 18 SER A 353 GLY A 355 5 3 HELIX 19 19 ARG A 366 GLY A 369 5 4 HELIX 20 20 ASP A 371 VAL A 382 1 12 HELIX 21 21 ALA A 407 ARG A 413 1 7 HELIX 22 22 ARG A 416 LYS A 440 1 25 HELIX 23 23 LYS A 443 ASP A 454 1 12 HELIX 24 24 ASP A 454 ALA A 474 1 21 HELIX 25 25 SER B 27 ASP B 32 1 6 HELIX 26 26 ASP B 32 GLY B 49 1 18 HELIX 27 27 SER B 60 GLY B 68 1 9 HELIX 28 28 SER B 69 LYS B 74 5 6 HELIX 29 29 ALA B 88 PHE B 106 1 19 HELIX 30 30 SER B 121 LEU B 134 1 14 HELIX 31 31 LEU B 145 GLY B 148 5 4 HELIX 32 32 HIS B 150 GLY B 154 5 5 HELIX 33 33 ALA B 164 PHE B 169 1 6 HELIX 34 34 ASP B 184 ARG B 196 1 13 HELIX 35 35 ASP B 212 LYS B 224 1 13 HELIX 36 36 ILE B 234 ALA B 240 1 7 HELIX 37 37 SER B 245 HIS B 249 5 5 HELIX 38 38 HIS B 258 ARG B 262 5 5 HELIX 39 39 THR B 289 PHE B 299 1 11 HELIX 40 40 HIS B 307 THR B 323 1 17 HELIX 41 41 THR B 323 GLU B 346 1 24 HELIX 42 42 SER B 353 GLY B 355 5 3 HELIX 43 43 ASP B 371 VAL B 382 1 12 HELIX 44 44 ALA B 407 ARG B 413 1 7 HELIX 45 45 ARG B 416 LYS B 440 1 25 HELIX 46 46 LYS B 443 ASP B 454 1 12 HELIX 47 47 ASP B 454 ALA B 474 1 21 SHEET 1 A 2 LEU A 50 GLU A 51 0 SHEET 2 A 2 ILE A 384 THR A 385 1 O THR A 385 N LEU A 50 SHEET 1 B 2 GLY A 78 TYR A 79 0 SHEET 2 B 2 LYS A 82 ARG A 83 -1 O LYS A 82 N TYR A 79 SHEET 1 C 7 TRP A 113 ASN A 116 0 SHEET 2 C 7 GLY A 267 ARG A 272 -1 O ILE A 269 N ASN A 116 SHEET 3 C 7 ILE A 252 THR A 256 -1 N VAL A 253 O PHE A 270 SHEET 4 C 7 HIS A 226 ASP A 230 1 N ALA A 229 O ILE A 252 SHEET 5 C 7 LEU A 199 ALA A 202 1 N ALA A 202 O LEU A 228 SHEET 6 C 7 ARG A 139 LEU A 143 1 N MET A 141 O ILE A 201 SHEET 7 C 7 GLU A 170 TYR A 174 1 O GLU A 170 N ILE A 140 SHEET 1 D 4 SER A 350 LEU A 351 0 SHEET 2 D 4 LEU A 360 ASP A 364 -1 O ASP A 364 N SER A 350 SHEET 3 D 4 GLY A 402 GLY A 406 -1 O LEU A 403 N VAL A 363 SHEET 4 D 4 ASN A 387 ASN A 389 -1 N ASN A 387 O ARG A 404 SHEET 1 E 2 LEU B 50 GLU B 51 0 SHEET 2 E 2 ILE B 384 THR B 385 1 O THR B 385 N LEU B 50 SHEET 1 F 2 GLY B 78 TYR B 79 0 SHEET 2 F 2 LYS B 82 ARG B 83 -1 O LYS B 82 N TYR B 79 SHEET 1 G 7 TRP B 113 ASN B 116 0 SHEET 2 G 7 GLY B 267 ARG B 272 -1 O ILE B 269 N ASN B 116 SHEET 3 G 7 ILE B 252 THR B 256 -1 N VAL B 253 O PHE B 270 SHEET 4 G 7 HIS B 226 ASP B 230 1 N ALA B 229 O ILE B 252 SHEET 5 G 7 LEU B 199 ALA B 202 1 N ILE B 200 O HIS B 226 SHEET 6 G 7 ARG B 139 LEU B 143 1 N MET B 141 O ILE B 201 SHEET 7 G 7 GLU B 170 TYR B 174 1 O GLU B 170 N ILE B 140 SHEET 1 H 4 SER B 350 LEU B 351 0 SHEET 2 H 4 LEU B 360 ASP B 364 -1 O ASP B 364 N SER B 350 SHEET 3 H 4 GLY B 402 GLY B 406 -1 O LEU B 403 N VAL B 363 SHEET 4 H 4 ASN B 387 ASN B 389 -1 N ASN B 387 O ARG B 404 LINK C HIS A 258 N LLP A 259 1555 1555 1.33 LINK C LLP A 259 N THR A 260 1555 1555 1.32 LINK C HIS B 258 N LLP B 259 1555 1555 1.33 LINK C LLP B 259 N THR B 260 1555 1555 1.32 CISPEP 1 PHE A 299 PRO A 300 0 12.34 CISPEP 2 PHE B 299 PRO B 300 0 13.04 SITE 1 AC1 9 SER A 55 HIS A 150 HIS A 233 LLP A 259 SITE 2 AC1 9 ARG A 404 TYR B 75 GLU B 77 TYR B 85 SITE 3 AC1 9 HOH B 628 SITE 1 AC2 7 ARG A 209 LEU A 210 ILE A 211 TYR A 213 SITE 2 AC2 7 ILE A 234 PRO A 244 ASN A 358 SITE 1 AC3 7 TYR A 75 GLU A 77 TYR A 85 SER B 55 SITE 2 AC3 7 HIS B 233 LLP B 259 ARG B 404 CRYST1 160.462 160.462 211.461 90.00 90.00 120.00 P 65 2 2 24 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 0.006232 0.003598 0.000000 0.00000 SCALE2 0.000000 0.007196 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004729 0.00000