HEADER HYDROLASE/HYDROLASE INHIBITOR 11-MAY-05 1X3Z 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 EC: 3.5.1.52; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UV EXCISION REPAIR PROTEIN RAD23; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: XPC BINDING DOMAIN; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PEPTIDE PHQ-VAL-ALA-ASP-CF0; COMPND 13 CHAIN: I; COMPND 14 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; SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.-H.LEE,J.M.CHOI,C.LEE,K.J.YI,Y.CHO REVDAT 5 29-JUL-20 1X3Z 1 COMPND REMARK HET HETNAM REVDAT 5 2 1 FORMUL LINK SITE ATOM REVDAT 4 13-JUL-11 1X3Z 1 VERSN REVDAT 3 24-FEB-09 1X3Z 1 VERSN REVDAT 2 28-JUN-05 1X3Z 1 JRNL REVDAT 1 14-JUN-05 1X3Z 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. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 28388 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1471 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1872 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.4240 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.4110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3121 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.34000 REMARK 3 B22 (A**2) : 3.34000 REMARK 3 B33 (A**2) : -5.01000 REMARK 3 B12 (A**2) : 1.67000 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): 0.260 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.222 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.524 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3239 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4385 ; 1.644 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 377 ; 7.140 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;40.756 ;24.706 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 569 ;24.366 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;22.802 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 477 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2457 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1882 ; 0.279 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2235 ; 0.334 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 151 ; 0.200 ; 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): 20 ; 0.219 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.158 ; 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): 1934 ; 1.044 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3064 ; 1.891 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1470 ; 3.454 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1321 ; 3.281 ; 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): 3404 ; 4.222 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 30 ; 3.905 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3168 ; 1.737 ; 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 1X3Z 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_1000024349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-05 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 : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0721 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : KODAK REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30868 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : NULL 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) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 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: MOLECULAR REPLACEMENT 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, HANGING DROP, TEMPERATURE 277K 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 42.79200 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 85.58400 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 85.58400 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 42.79200 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 THE 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, I, C, D 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE N-[(BENZYLOXY)CARBONYL]-L-VALYL-N-[(1S)-1-(CARBOXYMETHYL)-3- REMARK 400 FLUORO-2-OXOPROPYL]-L-ALANINAMIDE IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: N-[(BENZYLOXY)CARBONYL]-L-VALYL-N-[(1S)-1-(CARBOXYMETHYL)-3- REMARK 400 FLUORO-2-OXOPROPYL]-L-ALANINAMIDE REMARK 400 CHAIN: I REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 465 PHQ I 0 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 OE1 GLU A 216 N SER A 256 2.03 REMARK 500 O PHE A 26 OG SER A 29 2.14 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 CYS A 258 CB CYS A 258 SG -0.121 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 40.40 179.70 REMARK 500 ILE A 10 -46.20 -14.99 REMARK 500 ASP A 11 127.24 31.71 REMARK 500 LEU A 20 -39.26 -39.06 REMARK 500 LYS A 32 -137.79 -101.07 REMARK 500 LYS A 33 127.40 -18.02 REMARK 500 ALA A 34 42.30 -86.76 REMARK 500 ALA A 35 120.89 -22.17 REMARK 500 ASN A 39 -37.42 -35.28 REMARK 500 PHE A 42 -71.55 -56.16 REMARK 500 HIS A 61 -74.12 -86.97 REMARK 500 THR A 64 -35.70 -142.67 REMARK 500 ASP A 67 77.32 -106.88 REMARK 500 HIS A 97 -78.78 -85.54 REMARK 500 GLU A 99 -69.32 39.46 REMARK 500 ASN A 102 2.38 -64.76 REMARK 500 CYS A 132 -166.73 -64.25 REMARK 500 ASN A 135 44.26 -87.33 REMARK 500 SER A 137 55.22 -155.08 REMARK 500 GLU A 138 -30.59 -150.90 REMARK 500 ASN A 139 35.74 -71.58 REMARK 500 ASN A 149 14.94 -68.38 REMARK 500 PHE A 155 -164.97 -103.68 REMARK 500 ASN A 156 63.53 -102.28 REMARK 500 THR A 159 135.88 -175.77 REMARK 500 ARG A 190 -168.10 -108.63 REMARK 500 ASN A 196 -70.42 -42.33 REMARK 500 ASP A 217 58.98 37.70 REMARK 500 CYS A 237 -72.81 -69.25 REMARK 500 ASP A 242 73.51 57.11 REMARK 500 GLN A 243 71.00 -158.55 REMARK 500 ILE A 246 -62.55 -21.20 REMARK 500 SER A 256 -70.57 -113.53 REMARK 500 GLN A 276 -169.59 -160.47 REMARK 500 ASP A 282 19.74 173.33 REMARK 500 LYS A 290 -75.79 -51.17 REMARK 500 SER A 303 56.66 -119.00 REMARK 500 LEU B 262 -28.34 -37.40 REMARK 500 ASN B 272 57.59 -150.07 REMARK 500 GLU B 281 -74.12 -66.20 REMARK 500 ALA B 285 26.13 -70.38 REMARK 500 ARG B 286 -25.05 -155.10 REMARK 500 TYR B 287 71.54 -117.65 REMARK 500 PRO B 288 -63.51 -23.11 REMARK 500 ARG B 291 -30.51 -35.20 REMARK 500 ASN B 297 93.54 139.06 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 ASP A 11 PHE A 12 -139.23 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 109.7 REMARK 620 3 CYS A 165 SG 95.7 111.7 REMARK 620 4 CYS A 168 SG 110.0 117.4 110.1 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1X3W RELATED DB: PDB REMARK 900 PEPTIDE:N-GLYCANASE-RAD23 COMPLEX DBREF 1X3Z A 8 342 GB 6325161 NP_015229 8 342 DBREF 1X3Z B 238 309 UNP P32628 RAD23_YEAST 238 309 DBREF 1X3Z I 0 4 PDB 1X3Z 1X3Z 0 4 SEQRES 1 A 335 ASN ASN ILE ASP PHE ASP SER ILE ALA LYS MET 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 MET 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 MET 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 MET ALA ASN PRO GLU VAL PHE VAL SEQRES 6 B 72 SER MET LEU LEU GLU ALA VAL SEQRES 1 I 5 PHQ VAL ALA ASP CF0 HET CF0 I 4 1 HET GLC C 1 11 HET FRU C 2 12 HET GLC D 1 11 HET FRU D 2 12 HET ZN A 999 1 HETNAM CF0 FLUOROMETHANE HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM ZN ZINC ION HETSYN CF0 FLUORO METHYL GROUP FORMUL 3 CF0 C H3 F FORMUL 4 GLC 2(C6 H12 O6) FORMUL 4 FRU 2(C6 H12 O6) FORMUL 6 ZN ZN 2+ FORMUL 7 HOH *29(H2 O) HELIX 1 1 PHE A 12 PHE A 31 1 20 HELIX 2 2 ALA A 35 ASN A 49 1 15 HELIX 3 3 ASN A 49 TYR A 66 1 18 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 ASP A 119 1 18 HELIX 7 7 GLY A 150 LYS A 154 5 5 HELIX 8 8 ASP A 179 ARG A 187 1 9 HELIX 9 9 ARG A 190 SER A 204 1 15 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 ASN A 305 ARG A 325 1 21 HELIX 13 13 GLU B 260 ASN B 272 1 13 HELIX 14 14 ALA B 275 ALA B 285 1 11 HELIX 15 15 TYR B 287 ALA B 296 1 10 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 MET A 140 GLN A 146 0 SHEET 2 B 3 CYS A 157 CYS A 165 -1 O LYS A 164 N THR A 141 SHEET 3 B 3 ILE A 171 TYR A 177 -1 O THR A 172 N TYR A 163 SHEET 1 C 6 SER A 240 PHE A 241 0 SHEET 2 C 6 ARG A 230 ASP A 235 -1 N ASP A 235 O SER A 240 SHEET 3 C 6 HIS A 218 SER A 225 -1 N CYS A 221 O VAL A 234 SHEET 4 C 6 VAL A 209 ASN A 214 -1 N ARG A 210 O GLU A 222 SHEET 5 C 6 CYS A 258 GLY A 262 -1 O PHE A 261 N TYR A 211 SHEET 6 C 6 GLY A 265 ASP A 268 -1 O VAL A 267 N ALA A 260 LINK SG CYS A 191 C1 CF0 I 4 1555 1555 1.68 LINK C ASP I 3 C1 CF0 I 4 1555 1555 1.25 LINK C1 GLC C 1 O2 FRU C 2 1555 1555 1.42 LINK C1 GLC D 1 O2 FRU D 2 1555 1555 1.46 LINK SG CYS A 129 ZN ZN A 999 1555 1555 2.27 LINK SG CYS A 132 ZN ZN A 999 1555 1555 2.12 LINK SG CYS A 165 ZN ZN A 999 1555 1555 2.26 LINK SG CYS A 168 ZN ZN A 999 1555 1555 2.26 CRYST1 128.801 128.801 128.376 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 0.007764 0.004482 0.000000 0.00000 SCALE2 0.000000 0.008965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007790 0.00000