HEADER TRANSFERASE 10-DEC-12 3ZF8 TITLE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE MNN9 IN TITLE 2 COMPLEX WITH GDP AND MN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNAN POLYMERASE COMPLEXES SUBUNIT MNN9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GLOBULAR DOMAIN, RESIDUES 93-395; COMPND 5 SYNONYM: M-POL I SUBUNIT MNN9, M-POL II SUBUNIT MNN9; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: S288C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: PLYSS KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.STRIEBECK,A.W.SCHUETTELKOPF,D.M.F.VAN AALTEN REVDAT 1 25-SEP-13 3ZF8 0 JRNL AUTH A.STRIEBECK,D.A.ROBINSON,A.W.SCHUETTELKOPF,D.M.F.VAN AALTEN JRNL TITL YEAST MNN9 IS BOTH A PRIMING GLYCOSYLTRANSFERASE AND AN JRNL TITL 2 ALLOSTERIC ACTIVATOR OF MANNAN BIOSYNTHESIS. JRNL REF OPEN BIOL. V. 3 30022 2013 JRNL REFN ISSN 2046-2441 JRNL PMID 24026536 JRNL DOI 10.1098/RSOB.130022 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.97 REMARK 3 NUMBER OF REFLECTIONS : 23134 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) : 0.19066 REMARK 3 R VALUE (WORKING SET) : 0.18966 REMARK 3 FREE R VALUE : 0.23920 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.1 REMARK 3 FREE R VALUE TEST SET COUNT : 501 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) : 1.979 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.030 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1378 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.227 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.317 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2329 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.075 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.44 REMARK 3 B22 (A**2) : 1.44 REMARK 3 B33 (A**2) : -2.16 REMARK 3 B12 (A**2) : 0.72 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.201 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2414 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3278 ; 1.429 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 286 ; 6.979 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;35.600 ;24.711 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 412 ;15.628 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;19.090 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 355 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1838 ; 0.013 ; 0.021 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 95 A 1396 REMARK 3 ORIGIN FOR THE GROUP (A): 2.9988 31.6191 11.1857 REMARK 3 T TENSOR REMARK 3 T11: 0.0111 T22: 0.0431 REMARK 3 T33: 0.0149 T12: 0.0143 REMARK 3 T13: -0.0028 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.1153 L22: 0.1109 REMARK 3 L33: 0.4311 L12: 0.0510 REMARK 3 L13: -0.0563 L23: 0.0386 REMARK 3 S TENSOR REMARK 3 S11: -0.0184 S12: -0.0061 S13: 0.0026 REMARK 3 S21: -0.0187 S22: 0.0190 S23: 0.0026 REMARK 3 S31: 0.0050 S32: 0.0160 S33: -0.0007 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 USED IF PRESENT REMARK 3 IN THE INPUT. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 3ZF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-12. REMARK 100 THE PDBE ID CODE IS EBI-55069. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (QUANTUM 315) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23775 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.00 REMARK 200 RESOLUTION RANGE LOW (A) : 55.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.7 REMARK 200 R MERGE (I) : 0.15 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.80 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 220.60667 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 110.30333 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 165.45500 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 55.15167 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 275.75833 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 220.60667 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 110.30333 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 55.15167 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 165.45500 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 275.75833 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: 6210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.2 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 0.500000 -0.866025 0.000000 28.54500 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 49.44139 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 55.15167 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 A2079 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 GLY A 91 REMARK 465 ALA A 92 REMARK 465 GLU A 93 REMARK 465 GLY A 94 REMARK 465 GLN A 190 REMARK 465 SER A 191 REMARK 465 PHE A 192 REMARK 465 ASP A 193 REMARK 465 LYS A 194 REMARK 465 LEU A 195 REMARK 465 MET A 196 REMARK 465 GLU A 197 REMARK 465 LYS A 198 REMARK 465 GLU A 199 REMARK 465 ARG A 200 REMARK 465 HIS A 201 REMARK 465 HIS A 395 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 NZ LYS A 162 OD1 ASN A 394 8675 2.18 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 186 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 186 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 349 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 349 NE - CZ - NH2 ANGL. DEV. = -5.3 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 GLU A 109 62.89 -107.21 REMARK 500 ASP A 173 -168.90 -79.99 REMARK 500 LEU A 203 -53.34 77.77 REMARK 500 ALA A 311 -113.71 39.11 REMARK 500 PRO A 315 114.17 -38.83 REMARK 500 CYS A 340 80.29 -161.74 REMARK 500 GLU A 364 -129.07 51.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU A 203 23.4 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL 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 MN A1396 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 389 NE2 REMARK 620 2 GDP A1395 O1B 83.5 REMARK 620 3 GDP A1395 O3A 143.1 64.6 REMARK 620 4 ASP A 238 OD2 99.8 151.4 100.3 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 GDP A1395 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1396 DBREF 3ZF8 A 93 395 UNP P39107 MNN9_YEAST 93 395 SEQADV 3ZF8 GLY A 91 UNP P39107 EXPRESSION TAG SEQADV 3ZF8 ALA A 92 UNP P39107 EXPRESSION TAG SEQADV 3ZF8 ASN A 236 UNP P39107 ASP 236 ENGINEERED MUTATION SEQRES 1 A 305 GLY ALA GLU GLY HIS ILE ALA HIS TYR ASP LEU ASN LYS SEQRES 2 A 305 LEU HIS SER THR SER GLU ALA ALA VAL ASN LYS GLU HIS SEQRES 3 A 305 ILE LEU ILE LEU THR PRO MET GLN THR PHE HIS GLN GLN SEQRES 4 A 305 TYR TRP ASP ASN LEU LEU GLN LEU ASN TYR PRO ARG GLU SEQRES 5 A 305 LEU ILE GLU LEU GLY PHE ILE THR PRO ARG THR ALA THR SEQRES 6 A 305 GLY ASP LEU ALA LEU LYS LYS LEU GLU ASN ALA ILE LYS SEQRES 7 A 305 LYS VAL GLN THR ASP LYS LYS THR GLN ARG PHE SER LYS SEQRES 8 A 305 ILE THR ILE LEU ARG GLN ASN SER GLN SER PHE ASP LYS SEQRES 9 A 305 LEU MET GLU LYS GLU ARG HIS ALA LEU ASP VAL GLN LYS SEQRES 10 A 305 GLU ARG ARG ALA ALA MET ALA LEU ALA ARG ASN GLU LEU SEQRES 11 A 305 LEU PHE SER THR ILE GLY PRO HIS THR SER TRP VAL LEU SEQRES 12 A 305 TRP LEU ASN ALA ASP ILE ILE GLU THR PRO PRO SER LEU SEQRES 13 A 305 ILE GLN ASP MET THR LYS HIS ASN LYS ALA ILE LEU ALA SEQRES 14 A 305 ALA ASN ILE TYR GLN ARG PHE TYR ASP GLU GLU LYS LYS SEQRES 15 A 305 GLN PRO SER ILE ARG PRO TYR ASP PHE ASN ASN TRP GLN SEQRES 16 A 305 GLU SER ASP THR GLY LEU GLU ILE ALA SER GLN MET GLY SEQRES 17 A 305 ASP ASP GLU ILE ILE VAL GLU GLY TYR ALA GLU ILE ALA SEQRES 18 A 305 THR TYR ARG PRO LEU MET ALA HIS PHE TYR ASP ALA ASN SEQRES 19 A 305 GLY VAL PRO GLY GLU GLU MET ALA LEU ASP GLY VAL GLY SEQRES 20 A 305 GLY GLY CYS THR LEU VAL LYS ALA GLU VAL HIS ARG ASP SEQRES 21 A 305 GLY ALA MET PHE PRO ASN PHE PRO PHE TYR HIS LEU ILE SEQRES 22 A 305 GLU THR GLU GLY PHE ALA LYS MET ALA LYS ARG LEU ASN SEQRES 23 A 305 TYR ASP VAL PHE GLY LEU PRO ASN TYR LEU VAL TYR HIS SEQRES 24 A 305 ILE GLU GLU GLU ASN HIS HET GDP A1395 28 HET MN A1396 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MN MANGANESE (II) ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MN MN 2+ FORMUL 4 HOH *148(H2 O) HELIX 1 1 ASP A 100 LEU A 104 5 5 HELIX 2 2 HIS A 127 GLN A 136 1 10 HELIX 3 3 PRO A 140 GLU A 142 5 3 HELIX 4 4 THR A 153 THR A 172 1 20 HELIX 5 5 LYS A 174 ARG A 178 5 5 HELIX 6 6 LEU A 203 ILE A 225 1 23 HELIX 7 7 SER A 245 LYS A 252 1 8 HELIX 8 8 SER A 287 GLN A 296 1 10 HELIX 9 9 MET A 317 TYR A 321 5 5 HELIX 10 10 ALA A 345 ASP A 350 1 6 HELIX 11 11 ILE A 363 LEU A 375 1 13 SHEET 1 AA 7 LYS A 181 ARG A 186 0 SHEET 2 AA 7 ILE A 144 THR A 150 1 O LEU A 146 N THR A 183 SHEET 3 AA 7 HIS A 116 PRO A 122 1 O ILE A 117 N GLU A 145 SHEET 4 AA 7 THR A 229 LEU A 235 1 N SER A 230 O HIS A 116 SHEET 5 AA 7 CYS A 340 LYS A 344 -1 O THR A 341 N TRP A 234 SHEET 6 AA 7 ILE A 257 ASP A 268 -1 O LEU A 258 N LEU A 342 SHEET 7 AA 7 GLN A 273 PRO A 278 -1 O GLN A 273 N ASP A 268 SHEET 1 AB 8 LYS A 181 ARG A 186 0 SHEET 2 AB 8 ILE A 144 THR A 150 1 O LEU A 146 N THR A 183 SHEET 3 AB 8 HIS A 116 PRO A 122 1 O ILE A 117 N GLU A 145 SHEET 4 AB 8 THR A 229 LEU A 235 1 N SER A 230 O HIS A 116 SHEET 5 AB 8 CYS A 340 LYS A 344 -1 O THR A 341 N TRP A 234 SHEET 6 AB 8 ILE A 257 ASP A 268 -1 O LEU A 258 N LEU A 342 SHEET 7 AB 8 VAL A 379 HIS A 389 1 O PHE A 380 N ALA A 259 SHEET 8 AB 8 MET A 331 LEU A 333 1 O MET A 331 N GLY A 381 SHEET 1 AC 2 ILE A 239 GLU A 241 0 SHEET 2 AC 2 VAL A 379 HIS A 389 -1 O TYR A 388 N ILE A 240 SHEET 1 AD 8 LYS A 181 ARG A 186 0 SHEET 2 AD 8 ILE A 144 THR A 150 1 O LEU A 146 N THR A 183 SHEET 3 AD 8 HIS A 116 PRO A 122 1 O ILE A 117 N GLU A 145 SHEET 4 AD 8 THR A 229 LEU A 235 1 N SER A 230 O HIS A 116 SHEET 5 AD 8 CYS A 340 LYS A 344 -1 O THR A 341 N TRP A 234 SHEET 6 AD 8 ILE A 257 ASP A 268 -1 O LEU A 258 N LEU A 342 SHEET 7 AD 8 VAL A 379 HIS A 389 1 O PHE A 380 N ALA A 259 SHEET 8 AD 8 ILE A 239 GLU A 241 -1 N ILE A 240 O TYR A 388 SHEET 1 AE 2 GLN A 273 PRO A 278 0 SHEET 2 AE 2 ILE A 257 ASP A 268 -1 O GLN A 264 N ARG A 277 LINK MN MN A1396 NE2 HIS A 389 1555 1555 2.31 LINK MN MN A1396 O1B GDP A1395 1555 1555 2.22 LINK MN MN A1396 O3A GDP A1395 1555 1555 2.37 LINK MN MN A1396 OD2 ASP A 238 1555 1555 2.30 CISPEP 1 ALA A 202 LEU A 203 0 -8.05 SITE 1 AC1 16 PRO A 122 MET A 123 GLN A 124 ILE A 149 SITE 2 AC1 16 PRO A 151 GLN A 187 ARG A 209 MET A 213 SITE 3 AC1 16 ASN A 236 ALA A 237 ASP A 238 TYR A 279 SITE 4 AC1 16 HIS A 389 MN A1396 HOH A2029 HOH A2148 SITE 1 AC2 4 ASP A 238 HIS A 389 GDP A1395 HOH A2147 CRYST1 57.090 57.090 330.910 90.00 90.00 120.00 P 65 2 2 12 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 0.017516 0.010113 0.000000 0.00000 SCALE2 0.000000 0.020226 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003022 0.00000