HEADER HYDROLASE 06-OCT-08 3ESW TITLE COMPLEX OF YEAST PNGASE WITH GLCNAC2-IAC. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE-N(4)-(N-ACETYL-BETA-GLUCOSAMINYL)ASPARAGINE COMPND 3 AMIDASE; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: PEPTIDE:N-GLYCANASE; COMPND 6 SYNONYM: PNGASE, PEPTIDE:N-GLYCANASE 1, YPNG1; COMPND 7 EC: 3.5.1.52; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UV EXCISION REPAIR PROTEIN RAD23; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: XPCB DOMAIN; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: PNG1, YPL096W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3 CODON PLUS RIL; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 11 ORGANISM_COMMON: YEAST; SOURCE 12 ORGANISM_TAXID: 4932; SOURCE 13 GENE: RAD23, SYGP-ORF29, YEL037C; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21DE3 CODON PLUS RIL KEYWDS GLYCOPROTEINS PEPTIDE:N-GLYCANASE CHITOBIOSE, HYDROLASE, METAL- KEYWDS 2 BINDING, NUCLEUS, DNA DAMAGE, DNA REPAIR, PHOSPHOPROTEIN, UBL KEYWDS 3 CONJUGATION PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR G.ZHAO,X.ZHOU,W.J.LENNARZ,H.SCHINDELIN REVDAT 8 06-SEP-23 3ESW 1 HETSYN REVDAT 7 29-JUL-20 3ESW 1 COMPND REMARK SEQADV HETNAM REVDAT 7 2 1 LINK SITE ATOM REVDAT 6 25-OCT-17 3ESW 1 REMARK REVDAT 5 13-JUL-11 3ESW 1 VERSN REVDAT 4 09-JUN-09 3ESW 1 REVDAT REVDAT 3 24-FEB-09 3ESW 1 VERSN REVDAT 2 13-JAN-09 3ESW 1 JRNL REVDAT 1 11-NOV-08 3ESW 0 JRNL AUTH G.ZHAO,G.LI,X.ZHOU,I.MATSUO,Y.ITO,T.SUZUKI,W.J.LENNARZ, JRNL AUTH 2 H.SCHINDELIN JRNL TITL STRUCTURAL AND MUTATIONAL STUDIES ON THE IMPORTANCE OF JRNL TITL 2 OLIGOSACCHARIDE BINDING FOR THE ACTIVITY OF YEAST PNGASE. JRNL REF GLYCOBIOLOGY V. 19 118 2009 JRNL REFN ISSN 0959-6658 JRNL PMID 18854368 JRNL DOI 10.1093/GLYCOB/CWN108 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0054 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) : 3.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17961 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1084 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) : 3.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1468 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 2581 REMARK 3 BIN FREE R VALUE : 0.4550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3184 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 7 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) : 63.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.04000 REMARK 3 B22 (A**2) : 6.04000 REMARK 3 B33 (A**2) : -9.05000 REMARK 3 B12 (A**2) : 3.02000 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): 0.420 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.304 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.235 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.040 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3282 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2260 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4431 ; 1.599 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5485 ; 0.952 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 384 ; 8.674 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;35.589 ;24.593 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 580 ;22.011 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;19.061 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 475 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3610 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 672 ; 0.001 ; 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): 1930 ; 0.619 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 778 ; 0.067 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3119 ; 1.183 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1352 ; 1.236 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1312 ; 2.157 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -3 A 123 REMARK 3 RESIDUE RANGE : A 190 A 328 REMARK 3 ORIGIN FOR THE GROUP (A): 84.8747 47.4025 99.4067 REMARK 3 T TENSOR REMARK 3 T11: 0.0506 T22: 0.2253 REMARK 3 T33: 0.0527 T12: -0.0337 REMARK 3 T13: 0.0157 T23: 0.0211 REMARK 3 L TENSOR REMARK 3 L11: 1.4911 L22: 1.7729 REMARK 3 L33: 1.1080 L12: 1.2700 REMARK 3 L13: 1.0091 L23: 1.0022 REMARK 3 S TENSOR REMARK 3 S11: -0.2150 S12: 0.0175 S13: 0.0487 REMARK 3 S21: -0.1095 S22: 0.0850 S23: 0.1496 REMARK 3 S31: -0.1493 S32: 0.2709 S33: 0.1300 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 124 A 189 REMARK 3 ORIGIN FOR THE GROUP (A): 58.4383 35.8194 82.9119 REMARK 3 T TENSOR REMARK 3 T11: 0.0994 T22: 0.2311 REMARK 3 T33: 0.0510 T12: -0.1487 REMARK 3 T13: 0.0038 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 4.4614 L22: 0.7412 REMARK 3 L33: 9.2452 L12: -0.0351 REMARK 3 L13: 3.7951 L23: 1.6893 REMARK 3 S TENSOR REMARK 3 S11: 0.1354 S12: -0.2703 S13: 0.0298 REMARK 3 S21: -0.0783 S22: 0.1641 S23: -0.0985 REMARK 3 S31: 0.3401 S32: -0.4694 S33: -0.2995 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 : B 253 B 309 REMARK 3 ORIGIN FOR THE GROUP (A): 108.9646 60.0945 106.8493 REMARK 3 T TENSOR REMARK 3 T11: 0.0235 T22: 0.3482 REMARK 3 T33: 0.0421 T12: -0.0613 REMARK 3 T13: 0.0007 T23: -0.0337 REMARK 3 L TENSOR REMARK 3 L11: 9.2033 L22: 8.9565 REMARK 3 L33: 7.3019 L12: 3.0830 REMARK 3 L13: 1.4387 L23: 2.5715 REMARK 3 S TENSOR REMARK 3 S11: -0.1540 S12: -0.5147 S13: 0.5066 REMARK 3 S21: -0.3066 S22: 0.0341 S23: -0.1314 REMARK 3 S31: -0.2466 S32: 0.7333 S33: 0.1200 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 3ESW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17986 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 REMARK 200 RESOLUTION RANGE LOW (A) : 37.969 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : 0.12600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.4960 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.45700 REMARK 200 R SYM FOR SHELL (I) : 0.45700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1X3Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 81.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 8.5 AND 2.0 M REMARK 280 SODIUM CHLORIDE, EVAPORATION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 42.58367 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 85.16733 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 85.16733 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 42.58367 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 -13 REMARK 465 GLY A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 GLU A 330 REMARK 465 THR A 331 REMARK 465 LYS A 332 REMARK 465 SER A 333 REMARK 465 GLU A 334 REMARK 465 SER A 335 REMARK 465 VAL A 336 REMARK 465 SER A 337 REMARK 465 ALA A 338 REMARK 465 ALA A 339 REMARK 465 SER A 340 REMARK 465 LYS A 341 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 SER A -3 OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ILE A 15 O MET A 18 1.96 REMARK 500 O HIS A 233 O PHE A 241 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 190 C YCM A 191 N 0.189 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 190 CA - C - N ANGL. DEV. = 21.4 DEGREES REMARK 500 ARG A 190 O - C - N ANGL. DEV. = -32.1 DEGREES REMARK 500 YCM A 191 C - N - CA ANGL. DEV. = 16.2 DEGREES REMARK 500 YCM A 191 O - C - N ANGL. DEV. = -13.0 DEGREES REMARK 500 LEU B 306 CA - CB - CG ANGL. DEV. = 14.3 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 MET A 7 -154.65 -63.47 REMARK 500 ASN A 8 79.10 -52.79 REMARK 500 ASN A 9 97.22 -69.50 REMARK 500 LEU A 19 -65.05 109.42 REMARK 500 LYS A 32 -169.04 -127.65 REMARK 500 LYS A 33 -96.69 31.19 REMARK 500 ALA A 34 45.75 96.83 REMARK 500 PRO A 36 -19.30 -42.89 REMARK 500 VAL A 37 -75.40 -41.71 REMARK 500 ALA A 93 -71.63 -52.07 REMARK 500 LYS A 94 99.16 -49.71 REMARK 500 ASP A 95 139.60 -31.32 REMARK 500 HIS A 97 154.97 32.14 REMARK 500 ASN A 125 -81.69 -78.93 REMARK 500 GLN A 134 -76.12 -78.86 REMARK 500 ASN A 135 96.91 -65.48 REMARK 500 THR A 136 33.12 -173.79 REMARK 500 PHE A 155 30.71 -97.61 REMARK 500 ASN A 156 71.64 57.59 REMARK 500 CYS A 168 -21.26 -145.95 REMARK 500 YCM A 191 -87.58 -1.39 REMARK 500 GLU A 216 58.11 -93.24 REMARK 500 ASN A 229 78.31 -35.86 REMARK 500 GLN A 239 38.36 36.48 REMARK 500 GLN A 243 46.53 -141.83 REMARK 500 ILE A 246 -62.36 -14.30 REMARK 500 ILE A 249 -60.34 -98.00 REMARK 500 SER A 256 -61.06 -109.37 REMARK 500 GLN A 276 162.74 145.70 REMARK 500 ILE A 284 127.99 -175.19 REMARK 500 LEU B 263 -74.77 -62.66 REMARK 500 VAL B 269 9.44 -59.85 REMARK 500 SER B 270 12.69 -151.89 REMARK 500 ASN B 272 74.24 -157.18 REMARK 500 ASN B 297 108.05 -169.69 REMARK 500 LEU B 306 15.25 -65.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A -2 GLY A -1 31.96 REMARK 500 GLY A -1 LEU A 0 133.43 REMARK 500 YCM A 191 GLY A 192 140.43 REMARK 500 LEU A 228 ASN A 229 -143.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ARG A 190 29.76 REMARK 500 REMARK 500 REMARK: NULL DBREF 3ESW A 8 341 UNP Q02890 PNG1_YEAST 8 341 DBREF 3ESW B 254 308 UNP P32628 RAD23_YEAST 254 308 SEQADV 3ESW MET A -13 UNP Q02890 EXPRESSION TAG SEQADV 3ESW GLY A -12 UNP Q02890 EXPRESSION TAG SEQADV 3ESW SER A -11 UNP Q02890 EXPRESSION TAG SEQADV 3ESW SER A -10 UNP Q02890 EXPRESSION TAG SEQADV 3ESW HIS A -9 UNP Q02890 EXPRESSION TAG SEQADV 3ESW HIS A -8 UNP Q02890 EXPRESSION TAG SEQADV 3ESW HIS A -7 UNP Q02890 EXPRESSION TAG SEQADV 3ESW HIS A -6 UNP Q02890 EXPRESSION TAG SEQADV 3ESW HIS A -5 UNP Q02890 EXPRESSION TAG SEQADV 3ESW HIS A -4 UNP Q02890 EXPRESSION TAG SEQADV 3ESW SER A -3 UNP Q02890 EXPRESSION TAG SEQADV 3ESW SER A -2 UNP Q02890 EXPRESSION TAG SEQADV 3ESW GLY A -1 UNP Q02890 EXPRESSION TAG SEQADV 3ESW LEU A 0 UNP Q02890 EXPRESSION TAG SEQADV 3ESW VAL A 1 UNP Q02890 EXPRESSION TAG SEQADV 3ESW PRO A 2 UNP Q02890 EXPRESSION TAG SEQADV 3ESW ARG A 3 UNP Q02890 EXPRESSION TAG SEQADV 3ESW GLY A 4 UNP Q02890 EXPRESSION TAG SEQADV 3ESW SER A 5 UNP Q02890 EXPRESSION TAG SEQADV 3ESW HIS A 6 UNP Q02890 EXPRESSION TAG SEQADV 3ESW MET A 7 UNP Q02890 EXPRESSION TAG SEQRES 1 A 355 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 355 LEU VAL PRO ARG GLY SER HIS MET ASN ASN ILE ASP PHE SEQRES 3 A 355 ASP SER ILE ALA LYS MET LEU LEU ILE LYS TYR LYS ASP SEQRES 4 A 355 PHE ILE LEU SER LYS PHE LYS LYS ALA ALA PRO VAL GLU SEQRES 5 A 355 ASN ILE ARG PHE GLN ASN LEU VAL HIS THR ASN GLN PHE SEQRES 6 A 355 ALA GLN GLY VAL LEU GLY GLN SER GLN HIS LEU CYS THR SEQRES 7 A 355 VAL TYR ASP ASN PRO SER TRP HIS SER ILE VAL LEU GLU SEQRES 8 A 355 THR LEU ASP LEU ASP LEU ILE TYR LYS ASN VAL ASP LYS SEQRES 9 A 355 GLU PHE ALA LYS ASP GLY HIS ALA GLU GLY GLU ASN ILE SEQRES 10 A 355 TYR THR ASP TYR LEU VAL LYS GLU LEU LEU ARG TYR PHE SEQRES 11 A 355 LYS GLN ASP PHE PHE LYS TRP CYS ASN LYS PRO ASP CYS SEQRES 12 A 355 ASN HIS CYS GLY GLN ASN THR SER GLU ASN MET THR PRO SEQRES 13 A 355 LEU GLY SER GLN GLY PRO ASN GLY GLU GLU SER LYS PHE SEQRES 14 A 355 ASN CYS GLY THR VAL GLU ILE TYR LYS CYS ASN ARG CYS SEQRES 15 A 355 GLY ASN ILE THR ARG PHE PRO ARG TYR ASN ASP PRO ILE SEQRES 16 A 355 LYS LEU LEU GLU THR ARG LYS GLY ARG YCM GLY GLU TRP SEQRES 17 A 355 CYS ASN LEU PHE THR LEU ILE LEU LYS SER PHE GLY LEU SEQRES 18 A 355 ASP VAL ARG TYR VAL TRP ASN ARG GLU ASP HIS VAL TRP SEQRES 19 A 355 CYS GLU TYR PHE SER ASN PHE LEU ASN ARG TRP VAL HIS SEQRES 20 A 355 VAL ASP SER CYS GLU GLN SER PHE ASP GLN PRO TYR ILE SEQRES 21 A 355 TYR SER ILE ASN TRP ASN LYS LYS MET SER TYR CYS ILE SEQRES 22 A 355 ALA PHE GLY LYS ASP GLY VAL VAL ASP VAL SER LYS ARG SEQRES 23 A 355 TYR ILE LEU GLN ASN GLU LEU PRO ARG ASP GLN ILE LYS SEQRES 24 A 355 GLU GLU ASP LEU LYS PHE LEU CYS GLN PHE ILE THR LYS SEQRES 25 A 355 ARG LEU ARG TYR SER LEU ASN ASP ASP GLU ILE TYR GLN SEQRES 26 A 355 LEU ALA CYS ARG ASP GLU GLN GLU GLN ILE GLU LEU ILE SEQRES 27 A 355 ARG GLY LYS THR GLN GLU THR LYS SER GLU SER VAL SER SEQRES 28 A 355 ALA ALA SER LYS SEQRES 1 B 55 SER ILE GLY LEU THR VAL GLU ASP LEU LEU SER LEU ARG SEQRES 2 B 55 GLN VAL VAL SER GLY ASN PRO GLU ALA LEU ALA PRO LEU SEQRES 3 B 55 LEU GLU ASN ILE SER ALA ARG TYR PRO GLN LEU ARG GLU SEQRES 4 B 55 HIS ILE MET ALA ASN PRO GLU VAL PHE VAL SER MET LEU SEQRES 5 B 55 LEU GLU ALA MODRES 3ESW YCM A 191 CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HET YCM A 191 10 HET NAG C 1 14 HET NAG C 2 14 HET ZN A 344 1 HETNAM YCM S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM ZN ZINC ION HETSYN YCM CYSTEINE-S-ACETAMIDE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 1 YCM C5 H10 N2 O3 S FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *7(H2 O) HELIX 1 1 ASP A 11 PHE A 31 1 21 HELIX 2 2 ALA A 35 ASN A 49 1 15 HELIX 3 3 ASN A 49 CYS A 63 1 15 HELIX 4 4 ASN A 68 LEU A 79 1 12 HELIX 5 5 ASP A 80 LYS A 94 1 15 HELIX 6 6 ASN A 102 ASP A 119 1 18 HELIX 7 7 ASN A 149 LYS A 154 1 6 HELIX 8 8 ASP A 179 ARG A 187 1 9 HELIX 9 9 ARG A 190 PHE A 205 1 16 HELIX 10 10 ASN A 226 ASN A 229 5 4 HELIX 11 11 PRO A 244 ILE A 249 1 6 HELIX 12 12 VAL A 269 ILE A 274 1 6 HELIX 13 13 LYS A 285 LEU A 300 1 16 HELIX 14 14 ASN A 305 ARG A 325 1 21 HELIX 15 15 THR B 258 VAL B 269 1 12 HELIX 16 16 ASN B 272 GLU B 274 5 3 HELIX 17 17 ALA B 275 TYR B 287 1 13 HELIX 18 18 TYR B 287 ASN B 297 1 11 HELIX 19 19 ASN B 297 LEU B 306 1 10 SHEET 1 A 2 LYS A 122 TRP A 123 0 SHEET 2 A 2 LYS A 188 GLY A 189 1 O GLY A 189 N LYS A 122 SHEET 1 B 3 MET A 140 GLN A 146 0 SHEET 2 B 3 CYS A 157 CYS A 165 -1 O VAL A 160 N GLN A 146 SHEET 3 B 3 ILE A 171 TYR A 177 -1 O PHE A 174 N GLU A 161 SHEET 1 C 5 ARG A 230 VAL A 234 0 SHEET 2 C 5 HIS A 218 SER A 225 -1 N TYR A 223 O VAL A 232 SHEET 3 C 5 VAL A 209 ASN A 214 -1 N VAL A 212 O TRP A 220 SHEET 4 C 5 CYS A 258 GLY A 262 -1 O ILE A 259 N TRP A 213 SHEET 5 C 5 GLY A 265 ASP A 268 -1 O VAL A 267 N ALA A 260 LINK C ARG A 190 N YCM A 191 1555 1555 1.53 LINK C YCM A 191 N GLY A 192 1555 1555 1.45 LINK NZ2 YCM A 191 C1 NAG C 1 1555 1555 1.79 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.85 CISPEP 1 SER B 254 ILE B 255 0 -9.38 CRYST1 131.530 131.530 127.751 90.00 90.00 120.00 P 31 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 0.007603 0.004389 0.000000 0.00000 SCALE2 0.000000 0.008779 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007828 0.00000