PDB Short entry for 1X3W HEADER HYDROLASE 11-MAY-05 1X3W TITLE STRUCTURE OF A PEPTIDE:N-GLYCANASE-RAD23 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE:N-GLYCANASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 8-342; COMPND 5 EC: 3.5.1.52; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UV EXCISION REPAIR PROTEIN RAD23; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: XPC BINDING DOMAIN; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 11 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 12 ORGANISM_TAXID: 4932; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROTEIN-PROTEIN COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.-H.LEE,J.M.CHOI,C.LEE,K.J.YI,Y.CHO REVDAT 4 29-JUL-20 1X3W 1 COMPND REMARK SEQADV HET REVDAT 4 2 1 HETNAM FORMUL LINK SITE REVDAT 4 3 1 ATOM REVDAT 3 24-FEB-09 1X3W 1 VERSN REVDAT 2 28-JUN-05 1X3W 1 JRNL REVDAT 1 14-JUN-05 1X3W 0 JRNL AUTH J.H.LEE,J.M.CHOI,C.LEE,K.J.YI,Y.CHO JRNL TITL STRUCTURE OF A PEPTIDE:N-GLYCANASE-RAD23 COMPLEX: INSIGHT JRNL TITL 2 INTO THE DEGLYCOSYLATION FOR DENATURED GLYCOPROTEINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 9144 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15964983 JRNL DOI 10.1073/PNAS.0502082102 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 22672 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1180 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1158 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.4200 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.4370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3100 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.40000 REMARK 3 B22 (A**2) : 5.40000 REMARK 3 B33 (A**2) : -8.10000 REMARK 3 B12 (A**2) : 2.70000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.319 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.265 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 37.386 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3243 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4394 ; 1.688 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 375 ; 7.129 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;41.459 ;24.675 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 567 ;23.857 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;20.629 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 482 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2441 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1965 ; 0.296 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2218 ; 0.343 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 174 ; 0.199 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 13 ; 0.183 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.078 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1912 ; 1.069 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3041 ; 1.939 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1495 ; 3.953 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1353 ; 3.435 ; 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): 3407 ; 5.017 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 18 ; 4.378 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3170 ; 1.945 ; 3.000 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 : 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 REMARK 4 REMARK 4 1X3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25391 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 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) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32000 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: SAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 81.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE, MES, PH 6, VAPOR REMARK 280 DIFFUSION, 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 42.83133 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 85.66267 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 85.66267 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 42.83133 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS PROTEIN-PROTEIN COMPLEX IN REMARK 300 ASYMMETRIC UNIT 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: 3470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 THR A 328 REMARK 465 GLN A 329 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 465 SER A 342 REMARK 465 GLY B 238 REMARK 465 THR B 239 REMARK 465 THR B 240 REMARK 465 GLY B 241 REMARK 465 GLY B 242 REMARK 465 ALA B 243 REMARK 465 THR B 244 REMARK 465 ASP B 245 REMARK 465 ALA B 246 REMARK 465 ALA B 247 REMARK 465 GLN B 248 REMARK 465 GLY B 249 REMARK 465 GLY B 250 REMARK 465 PRO B 251 REMARK 465 PRO B 252 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 HIS A 233 O PHE A 241 2.05 REMARK 500 O ASP A 235 O GLU A 238 2.10 REMARK 500 O THR A 64 N TYR A 66 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 GLU A 77 CG GLU A 77 CD 0.090 REMARK 500 GLU A 185 CG GLU A 185 CD 0.106 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 ASN A 9 48.27 -171.76 REMARK 500 ALA A 16 -70.29 -62.20 REMARK 500 LEU A 20 -46.12 -28.01 REMARK 500 LYS A 33 137.78 51.81 REMARK 500 ASN A 39 -39.03 -39.58 REMARK 500 HIS A 61 -74.82 -84.42 REMARK 500 THR A 64 -92.01 -131.83 REMARK 500 VAL A 65 -48.21 27.47 REMARK 500 ASP A 67 61.20 -114.31 REMARK 500 SER A 70 -73.84 -37.40 REMARK 500 LYS A 94 -74.61 -44.89 REMARK 500 ASP A 95 -64.12 -109.47 REMARK 500 HIS A 97 -104.23 -27.81 REMARK 500 ALA A 98 -104.23 -91.17 REMARK 500 LYS A 117 -73.37 -77.71 REMARK 500 GLN A 118 40.04 -76.50 REMARK 500 ASP A 119 -59.75 -173.22 REMARK 500 ASN A 125 -70.96 -85.65 REMARK 500 ASN A 130 -72.44 -68.75 REMARK 500 CYS A 132 -160.57 -63.12 REMARK 500 GLU A 138 -60.78 -24.71 REMARK 500 ASN A 139 53.38 -92.97 REMARK 500 GLU A 185 -60.63 -94.00 REMARK 500 ARG A 190 -152.71 -82.78 REMARK 500 ASN A 196 -66.31 -22.88 REMARK 500 GLU A 216 57.84 -90.50 REMARK 500 ASN A 229 78.17 32.96 REMARK 500 ILE A 246 -79.12 11.61 REMARK 500 ILE A 274 75.33 -62.99 REMARK 500 LEU A 275 54.25 -115.02 REMARK 500 GLN A 276 149.94 132.96 REMARK 500 ASP A 282 87.67 -177.73 REMARK 500 ILE A 284 134.35 -177.27 REMARK 500 ASN A 305 -172.45 -67.86 REMARK 500 GLU A 308 -57.52 -25.82 REMARK 500 LEU A 323 -72.45 -66.59 REMARK 500 SER B 254 -110.13 -2.80 REMARK 500 ILE B 255 -67.45 -91.38 REMARK 500 VAL B 259 -50.01 -25.56 REMARK 500 LEU B 263 -74.16 -59.13 REMARK 500 SER B 264 -58.82 -27.12 REMARK 500 LEU B 265 -71.24 -40.62 REMARK 500 ASN B 272 55.57 -154.77 REMARK 500 GLU B 281 -80.73 -73.60 REMARK 500 TYR B 287 76.63 -118.96 REMARK 500 PRO B 288 -68.14 -24.05 REMARK 500 ALA B 296 -72.95 -79.98 REMARK 500 SER B 303 -79.50 -35.10 REMARK 500 MSE B 304 1.73 -53.67 REMARK 500 LEU B 305 -70.78 -91.84 REMARK 500 REMARK 500 THIS ENTRY HAS 51 RAMACHANDRAN OUTLIERS. 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 ZN A 999 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 129 SG REMARK 620 2 CYS A 132 SG 117.5 REMARK 620 3 CYS A 165 SG 88.4 95.6 REMARK 620 4 CYS A 168 SG 108.9 132.6 94.6 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1X3Z RELATED DB: PDB REMARK 900 PEPTIDE:N-GLYCANASE-RAD23 COMPLEX DBREF 1X3W A 8 342 UNP Q02890 Q02890_YEAST 8 342 DBREF 1X3W B 238 309 UNP P32628 RAD23_YEAST 238 309 SEQADV 1X3W MSE A 18 UNP Q02890 MET 18 MODIFIED RESIDUE SEQADV 1X3W MSE A 140 UNP Q02890 MET 140 MODIFIED RESIDUE SEQADV 1X3W MSE A 255 UNP Q02890 MET 255 MODIFIED RESIDUE SEQADV 1X3W MSE B 295 UNP P32628 MET 295 MODIFIED RESIDUE SEQADV 1X3W MSE B 304 UNP P32628 MET 304 MODIFIED RESIDUE SEQRES 1 A 335 ASN ASN ILE ASP PHE ASP SER ILE ALA LYS MSE LEU LEU SEQRES 2 A 335 ILE LYS TYR LYS ASP PHE ILE LEU SER LYS PHE LYS LYS SEQRES 3 A 335 ALA ALA PRO VAL GLU ASN ILE ARG PHE GLN ASN LEU VAL SEQRES 4 A 335 HIS THR ASN GLN PHE ALA GLN GLY VAL LEU GLY GLN SER SEQRES 5 A 335 GLN HIS LEU CYS THR VAL TYR ASP ASN PRO SER TRP HIS SEQRES 6 A 335 SER ILE VAL LEU GLU THR LEU ASP LEU ASP LEU ILE TYR SEQRES 7 A 335 LYS ASN VAL ASP LYS GLU PHE ALA LYS ASP GLY HIS ALA SEQRES 8 A 335 GLU GLY GLU ASN ILE TYR THR ASP TYR LEU VAL LYS GLU SEQRES 9 A 335 LEU LEU ARG TYR PHE LYS GLN ASP PHE PHE LYS TRP CYS SEQRES 10 A 335 ASN LYS PRO ASP CYS ASN HIS CYS GLY GLN ASN THR SER SEQRES 11 A 335 GLU ASN MSE THR PRO LEU GLY SER GLN GLY PRO ASN GLY SEQRES 12 A 335 GLU GLU SER LYS PHE ASN CYS GLY THR VAL GLU ILE TYR SEQRES 13 A 335 LYS CYS ASN ARG CYS GLY ASN ILE THR ARG PHE PRO ARG SEQRES 14 A 335 TYR ASN ASP PRO ILE LYS LEU LEU GLU THR ARG LYS GLY SEQRES 15 A 335 ARG CYS GLY GLU TRP CYS ASN LEU PHE THR LEU ILE LEU SEQRES 16 A 335 LYS SER PHE GLY LEU ASP VAL ARG TYR VAL TRP ASN ARG SEQRES 17 A 335 GLU ASP HIS VAL TRP CYS GLU TYR PHE SER ASN PHE LEU SEQRES 18 A 335 ASN ARG TRP VAL HIS VAL ASP SER CYS GLU GLN SER PHE SEQRES 19 A 335 ASP GLN PRO TYR ILE TYR SER ILE ASN TRP ASN LYS LYS SEQRES 20 A 335 MSE SER TYR CYS ILE ALA PHE GLY LYS ASP GLY VAL VAL SEQRES 21 A 335 ASP VAL SER LYS ARG TYR ILE LEU GLN ASN GLU LEU PRO SEQRES 22 A 335 ARG ASP GLN ILE LYS GLU GLU ASP LEU LYS PHE LEU CYS SEQRES 23 A 335 GLN PHE ILE THR LYS ARG LEU ARG TYR SER LEU ASN ASP SEQRES 24 A 335 ASP GLU ILE TYR GLN LEU ALA CYS ARG ASP GLU GLN GLU SEQRES 25 A 335 GLN ILE GLU LEU ILE ARG GLY LYS THR GLN GLU THR LYS SEQRES 26 A 335 SER GLU SER VAL SER ALA ALA SER LYS SER SEQRES 1 B 72 GLY THR THR GLY GLY ALA THR ASP ALA ALA GLN GLY GLY SEQRES 2 B 72 PRO PRO GLY SER ILE GLY LEU THR VAL GLU ASP LEU LEU SEQRES 3 B 72 SER LEU ARG GLN VAL VAL SER GLY ASN PRO GLU ALA LEU SEQRES 4 B 72 ALA PRO LEU LEU GLU ASN ILE SER ALA ARG TYR PRO GLN SEQRES 5 B 72 LEU ARG GLU HIS ILE MSE ALA ASN PRO GLU VAL PHE VAL SEQRES 6 B 72 SER MSE LEU LEU GLU ALA VAL MODRES 1X3W MSE A 18 MET SELENOMETHIONINE MODRES 1X3W MSE A 140 MET SELENOMETHIONINE MODRES 1X3W MSE A 255 MET SELENOMETHIONINE MODRES 1X3W MSE B 295 MET SELENOMETHIONINE MODRES 1X3W MSE B 304 MET SELENOMETHIONINE HET MSE A 18 8 HET MSE A 140 8 HET MSE A 255 8 HET MSE B 295 8 HET MSE B 304 8 HET GLC C 1 11 HET FRU C 2 12 HET GLC D 1 11 HET FRU D 2 12 HET GLC E 1 11 HET FRU E 2 12 HET ZN A 999 1 HETNAM MSE SELENOMETHIONINE HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM ZN ZINC ION FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 3 GLC 3(C6 H12 O6) FORMUL 3 FRU 3(C6 H12 O6) FORMUL 6 ZN ZN 2+ FORMUL 7 HOH *17(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 ASP A 95 1 16 HELIX 6 6 ASN A 102 GLN A 118 1 17 HELIX 7 7 ILE A 181 GLU A 185 5 5 HELIX 8 8 ARG A 190 SER A 204 1 15 HELIX 9 9 TYR A 245 ASN A 250 1 6 HELIX 10 10 VAL A 269 ILE A 274 1 6 HELIX 11 11 LYS A 285 TYR A 302 1 18 HELIX 12 12 ASP A 307 ILE A 324 1 18 HELIX 13 13 THR B 258 ASN B 272 1 15 HELIX 14 14 ALA B 275 ARG B 286 1 12 HELIX 15 15 TYR B 287 ASN B 297 1 11 HELIX 16 16 ASN B 297 ALA B 308 1 12 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 MSE 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 ARG A 176 N THR A 159 SHEET 1 C 5 ARG A 230 VAL A 234 0 SHEET 2 C 5 HIS A 218 SER A 225 -1 N CYS A 221 O VAL A 234 SHEET 3 C 5 ASP A 208 ASN A 214 -1 N ASN A 214 O HIS A 218 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 GLY A 265 N GLY A 262 LINK C LYS A 17 N MSE A 18 1555 1555 1.33 LINK C MSE A 18 N LEU A 19 1555 1555 1.33 LINK C ASN A 139 N MSE A 140 1555 1555 1.33 LINK C MSE A 140 N THR A 141 1555 1555 1.33 LINK C LYS A 254 N MSE A 255 1555 1555 1.33 LINK C MSE A 255 N SER A 256 1555 1555 1.33 LINK C ILE B 294 N MSE B 295 1555 1555 1.34 LINK C MSE B 295 N ALA B 296 1555 1555 1.34 LINK C SER B 303 N MSE B 304 1555 1555 1.33 LINK C MSE B 304 N LEU B 305 1555 1555 1.33 LINK C1 GLC C 1 O2 FRU C 2 1555 1555 1.43 LINK C1 GLC D 1 O2 FRU D 2 1555 1555 1.45 LINK C1 GLC E 1 O2 FRU E 2 1555 1555 1.43 LINK SG CYS A 129 ZN ZN A 999 1555 1555 2.32 LINK SG CYS A 132 ZN ZN A 999 1555 1555 2.27 LINK SG CYS A 165 ZN ZN A 999 1555 1555 2.29 LINK SG CYS A 168 ZN ZN A 999 1555 1555 2.29 CRYST1 129.235 129.235 128.494 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 0.007738 0.004467 0.000000 0.00000 SCALE2 0.000000 0.008935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007782 0.00000