HEADER HYDROLASE/HYDROLASE INHIBITOR 23-NOV-05 2F4O TITLE THE MOUSE PNGASE-HR23 COMPLEX REVEALS A COMPLETE REMODULATION OF THE TITLE 2 PROTEIN-PROTEIN INTERFACE COMPARED TO ITS YEAST ORTHOLOGS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE N-GLYCANASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 164-450; COMPND 5 EC: 3.5.1.52; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: XP-C REPAIR COMPLEMENTING COMPLEX 58 KDA PROTEIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: XPCB DOMAIN, RESIDUES 273-332; COMPND 11 SYNONYM: MHR23B, UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG B P58; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: PHQ-VAL-ALA-ASP-CF0; COMPND 15 CHAIN: I; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 GENE: RAD23B, MHR23B; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS-RIL; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PTYB1; SOURCE 20 MOL_ID: 3; SOURCE 21 SYNTHETIC: YES KEYWDS GLYCOPROTEINS, UBIQUITIN-DEPENDENT PROTEIN DEGRADATION, NUCLEOTIDE KEYWDS 2 EXCISION REPAIR, PEPTIDE:N-GLYCANASE, TRANSGLUTAMINASE, HYDROLASE- KEYWDS 3 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.ZHAO,X.ZHOU,L.WANG,C.KISKER,W.J.LENNARZ,H.SCHINDELIN REVDAT 6 23-AUG-23 2F4O 1 REMARK SEQADV LINK REVDAT 5 18-OCT-17 2F4O 1 REMARK REVDAT 4 13-JUL-11 2F4O 1 VERSN REVDAT 3 24-FEB-09 2F4O 1 VERSN REVDAT 2 08-AUG-06 2F4O 1 JRNL REVDAT 1 07-MAR-06 2F4O 0 JRNL AUTH G.ZHAO,X.ZHOU,L.WANG,G.LI,C.KISKER,W.J.LENNARZ,H.SCHINDELIN JRNL TITL STRUCTURE OF THE MOUSE PEPTIDE N-GLYCANASE-HR23 COMPLEX JRNL TITL 2 SUGGESTS CO-EVOLUTION OF THE ENDOPLASMIC JRNL TITL 3 RETICULUM-ASSOCIATED DEGRADATION AND DNA REPAIR PATHWAYS. JRNL REF J.BIOL.CHEM. V. 281 13751 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16500903 JRNL DOI 10.1074/JBC.M600137200 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.2 REMARK 3 NUMBER OF REFLECTIONS : 14551 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 739 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) : 2.26 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 581 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 48.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2945 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 18 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) : 62.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.75000 REMARK 3 B22 (A**2) : 1.29000 REMARK 3 B33 (A**2) : -3.36000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.86000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.665 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.333 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.274 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.605 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3010 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2675 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4062 ; 1.559 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6246 ; 0.879 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 349 ; 8.003 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;38.358 ;24.198 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 547 ;18.783 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;18.514 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 431 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3307 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 612 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 725 ; 0.235 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2976 ; 0.197 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1418 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1766 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 75 ; 0.209 ; 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): 23 ; 0.286 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 44 ; 0.183 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.111 ; 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): 2292 ; 0.711 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 713 ; 0.144 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2859 ; 0.891 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1434 ; 1.408 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1203 ; 2.041 ; 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 273 B 333 REMARK 3 ORIGIN FOR THE GROUP (A): -43.2425 -14.4695 -7.4059 REMARK 3 T TENSOR REMARK 3 T11: -0.0794 T22: -0.1017 REMARK 3 T33: -0.1804 T12: -0.0764 REMARK 3 T13: 0.1524 T23: -0.0644 REMARK 3 L TENSOR REMARK 3 L11: 11.0712 L22: 6.7336 REMARK 3 L33: 9.0803 L12: 0.7874 REMARK 3 L13: -7.7772 L23: -0.6421 REMARK 3 S TENSOR REMARK 3 S11: -0.4133 S12: 0.1368 S13: -0.8587 REMARK 3 S21: 0.1045 S22: -0.0662 S23: 0.3896 REMARK 3 S31: 0.9268 S32: -0.8186 S33: 0.4795 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 164 A 241 REMARK 3 RESIDUE RANGE : A 292 A 458 REMARK 3 ORIGIN FOR THE GROUP (A): -27.5810 2.9828 -18.5852 REMARK 3 T TENSOR REMARK 3 T11: -0.1592 T22: -0.2353 REMARK 3 T33: -0.2720 T12: -0.0282 REMARK 3 T13: 0.0255 T23: -0.0340 REMARK 3 L TENSOR REMARK 3 L11: 3.8035 L22: 4.1567 REMARK 3 L33: 6.3476 L12: 1.7758 REMARK 3 L13: -2.0776 L23: -0.9609 REMARK 3 S TENSOR REMARK 3 S11: 0.2821 S12: -0.2577 S13: 0.5351 REMARK 3 S21: 0.2954 S22: -0.0542 S23: 0.1195 REMARK 3 S31: -0.8702 S32: 0.2750 S33: -0.2279 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 242 A 291 REMARK 3 RESIDUE RANGE : A 501 A 502 REMARK 3 ORIGIN FOR THE GROUP (A): -4.9831 4.6505 -37.1906 REMARK 3 T TENSOR REMARK 3 T11: -0.0630 T22: 0.2040 REMARK 3 T33: 0.0601 T12: -0.1074 REMARK 3 T13: 0.0168 T23: 0.0280 REMARK 3 L TENSOR REMARK 3 L11: 10.3214 L22: 1.9916 REMARK 3 L33: 3.4231 L12: 1.5904 REMARK 3 L13: -5.0609 L23: 0.5025 REMARK 3 S TENSOR REMARK 3 S11: -0.0497 S12: -0.6961 S13: -0.5154 REMARK 3 S21: -0.1445 S22: 0.1009 S23: -0.6872 REMARK 3 S31: 0.4615 S32: 0.4850 S33: -0.0512 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 2F4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035448. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17174 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23400 REMARK 200 R SYM FOR SHELL (I) : 0.21600 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2F4M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 28-32% PEG4000, 0.2 M REMARK 280 SODIUM ACETATE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K, PH 8.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 48.47900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.04850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.47900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.04850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: HETERODIMER COVALENTLY MODIFIED BY INHIBITOR. 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: 3030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, I 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -135.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, I 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 -1.000000 0.000000 0.000000 -64.71994 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -74.14247 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 ARG A 448 REMARK 465 PRO A 449 REMARK 465 GLY A 450 REMARK 465 LEU A 451 REMARK 465 GLU A 452 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 C ASP I 4 C1 CF0 I 5 1.49 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 199 CD GLU A 199 OE2 0.090 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 291 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 291 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 CYS A 306 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 ASP A 329 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 280 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 280 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP I 4 CB - CG - OD2 ANGL. DEV. = 6.0 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 GLN A 177 -70.46 -48.79 REMARK 500 SER A 198 -44.25 -25.70 REMARK 500 ASN A 219 -171.33 69.99 REMARK 500 SER A 221 129.38 70.45 REMARK 500 ASP A 222 -65.75 -156.00 REMARK 500 PHE A 238 -61.35 -95.68 REMARK 500 ASN A 243 -82.63 -85.90 REMARK 500 GLU A 253 135.01 -28.43 REMARK 500 GLU A 259 108.22 -57.87 REMARK 500 ASP A 265 -59.62 -177.10 REMARK 500 ARG A 291 79.26 -115.90 REMARK 500 ARG A 305 -155.59 -111.40 REMARK 500 THR A 331 32.98 -87.14 REMARK 500 TRP A 335 -154.08 -156.05 REMARK 500 SER A 371 -74.99 -139.42 REMARK 500 HIS A 454 -86.15 -55.06 REMARK 500 HIS A 455 96.18 -64.22 REMARK 500 HIS A 456 44.43 -106.31 REMARK 500 HIS A 457 -143.09 -128.00 REMARK 500 ARG B 308 -61.43 -90.67 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 HIS A 455 HIS A 456 141.63 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 247 SG REMARK 620 2 CYS A 250 SG 103.4 REMARK 620 3 CYS A 280 SG 106.9 109.4 REMARK 620 4 CYS A 283 SG 110.5 107.7 118.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 353 OE2 REMARK 620 2 HIS A 457 ND1 126.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF PHQ-VAL-ALA-ASP-CF0 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2F4M RELATED DB: PDB REMARK 900 THE MOUSE PNGASE-HR23 COMPLEX WITHOUT INHIBITOR DBREF 2F4O A 164 450 GB 30517852 AAP03060 164 450 DBREF 2F4O B 273 332 UNP P54728 RD23B_MOUSE 273 332 DBREF 2F4O I 1 5 PDB 2F4O 2F4O 1 5 SEQADV 2F4O LEU A 451 GB 30517852 CLONING ARTIFACT SEQADV 2F4O GLU A 452 GB 30517852 CLONING ARTIFACT SEQADV 2F4O HIS A 453 GB 30517852 EXPRESSION TAG SEQADV 2F4O HIS A 454 GB 30517852 EXPRESSION TAG SEQADV 2F4O HIS A 455 GB 30517852 EXPRESSION TAG SEQADV 2F4O HIS A 456 GB 30517852 EXPRESSION TAG SEQADV 2F4O HIS A 457 GB 30517852 EXPRESSION TAG SEQADV 2F4O HIS A 458 GB 30517852 EXPRESSION TAG SEQADV 2F4O GLY B 333 UNP P54728 CLONING ARTIFACT SEQRES 1 A 295 GLY ASP SER THR ILE LEU LYS VAL LEU GLN SER ASN ILE SEQRES 2 A 295 GLN HIS VAL GLN LEU TYR GLU ASN PRO VAL LEU GLN GLU SEQRES 3 A 295 LYS ALA LEU THR CYS ILE PRO VAL SER GLU LEU LYS ARG SEQRES 4 A 295 LYS ALA GLN GLU LYS LEU PHE ARG ALA ARG LYS LEU ASP SEQRES 5 A 295 LYS GLY THR ASN VAL SER ASP GLU ASP PHE LEU LEU LEU SEQRES 6 A 295 GLU LEU LEU HIS TRP PHE LYS GLU GLU PHE PHE ARG TRP SEQRES 7 A 295 VAL ASN ASN ILE VAL CYS SER LYS CYS GLY GLY GLU THR SEQRES 8 A 295 ARG SER ARG ASP GLU ALA LEU LEU PRO ASN ASP ASP GLU SEQRES 9 A 295 LEU LYS TRP GLY ALA LYS ASN VAL GLU ASN HIS TYR CYS SEQRES 10 A 295 ASP ALA CYS GLN LEU SER ASN ARG PHE PRO ARG TYR ASN SEQRES 11 A 295 ASN PRO GLU LYS LEU LEU GLU THR ARG CYS GLY ARG CYS SEQRES 12 A 295 GLY GLU TRP ALA ASN CYS PHE THR LEU CYS CYS ARG ALA SEQRES 13 A 295 LEU GLY PHE GLU ALA ARG TYR VAL TRP ASP TYR THR ASP SEQRES 14 A 295 HIS VAL TRP THR GLU VAL TYR SER PRO SER GLN GLN ARG SEQRES 15 A 295 TRP LEU HIS CYS ASP ALA CYS GLU ASP VAL CYS ASP LYS SEQRES 16 A 295 PRO LEU LEU TYR GLU ILE GLY TRP GLY LYS LYS LEU SER SEQRES 17 A 295 TYR ILE ILE ALA PHE SER LYS ASP GLU VAL VAL ASP VAL SEQRES 18 A 295 THR TRP ARG TYR SER CYS LYS HIS ASP GLU VAL MET SER SEQRES 19 A 295 ARG ARG THR LYS VAL LYS GLU GLU LEU LEU ARG GLU THR SEQRES 20 A 295 ILE ASN GLY LEU ASN LYS GLN ARG GLN LEU SER LEU SER SEQRES 21 A 295 GLU SER ARG ARG LYS GLU LEU LEU GLN ARG ILE ILE VAL SEQRES 22 A 295 GLU LEU VAL GLU PHE ILE SER PRO LYS THR PRO ARG PRO SEQRES 23 A 295 GLY LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 61 GLY HIS PRO LEU GLU PHE LEU ARG ASN GLN PRO GLN PHE SEQRES 2 B 61 GLN GLN MET ARG GLN ILE ILE GLN GLN ASN PRO SER LEU SEQRES 3 B 61 LEU PRO ALA LEU LEU GLN GLN ILE GLY ARG GLU ASN PRO SEQRES 4 B 61 GLN LEU LEU GLN GLN ILE SER GLN HIS GLN GLU HIS PHE SEQRES 5 B 61 ILE GLN MET LEU ASN GLU PRO VAL GLY SEQRES 1 I 5 PHQ VAL ALA ASP CF0 HET PHQ I 1 10 HET CF0 I 5 1 HET ZN A 501 1 HET ZN A 502 1 HET CL A 1 1 HETNAM PHQ BENZYL CHLOROCARBONATE HETNAM CF0 FLUOROMETHANE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETSYN CF0 FLUORO METHYL GROUP FORMUL 3 PHQ C8 H7 CL O2 FORMUL 3 CF0 C H3 F FORMUL 4 ZN 2(ZN 2+) FORMUL 6 CL CL 1- FORMUL 7 HOH *18(H2 O) HELIX 1 1 SER A 166 VAL A 179 1 14 HELIX 2 2 GLN A 180 GLU A 183 5 4 HELIX 3 3 ASN A 184 ALA A 191 1 8 HELIX 4 4 PRO A 196 ARG A 212 1 17 HELIX 5 5 ASP A 222 GLU A 237 1 16 HELIX 6 6 ASP A 265 TRP A 270 1 6 HELIX 7 7 ASN A 294 ARG A 302 1 9 HELIX 8 8 ARG A 305 LEU A 320 1 16 HELIX 9 9 LYS A 358 TYR A 362 5 5 HELIX 10 10 THR A 385 SER A 389 5 5 HELIX 11 11 LYS A 391 ARG A 399 1 9 HELIX 12 12 LYS A 403 ARG A 418 1 16 HELIX 13 13 SER A 423 ILE A 442 1 20 HELIX 14 14 LEU B 276 ARG B 280 5 5 HELIX 15 15 GLN B 282 GLN B 294 1 13 HELIX 16 16 ASN B 295 SER B 297 5 3 HELIX 17 17 LEU B 298 ASN B 310 1 13 HELIX 18 18 ASN B 310 HIS B 320 1 11 HELIX 19 19 HIS B 320 ASN B 329 1 10 SHEET 1 A 2 ARG A 240 TRP A 241 0 SHEET 2 A 2 CYS A 303 GLY A 304 1 O GLY A 304 N ARG A 240 SHEET 1 B 3 ARG A 255 LEU A 261 0 SHEET 2 B 3 ALA A 272 CYS A 280 -1 O TYR A 279 N ARG A 255 SHEET 3 B 3 LEU A 285 TYR A 292 -1 O ASN A 287 N HIS A 278 SHEET 1 C 6 VAL A 355 CYS A 356 0 SHEET 2 C 6 ARG A 345 ASP A 350 -1 N ASP A 350 O VAL A 355 SHEET 3 C 6 HIS A 333 SER A 340 -1 N THR A 336 O CYS A 349 SHEET 4 C 6 ALA A 324 ASP A 329 -1 N ARG A 325 O GLU A 337 SHEET 5 C 6 ILE A 373 PHE A 376 -1 O ILE A 374 N TRP A 328 SHEET 6 C 6 VAL A 381 ASP A 383 -1 O VAL A 382 N ALA A 375 LINK SG CYS A 306 C1 CF0 I 5 1555 1555 1.52 LINK C1 PHQ I 1 N VAL I 2 1555 1555 1.36 LINK SG CYS A 247 ZN ZN A 501 1555 1555 2.52 LINK SG CYS A 250 ZN ZN A 501 1555 1555 2.23 LINK SG CYS A 280 ZN ZN A 501 1555 1555 2.28 LINK SG CYS A 283 ZN ZN A 501 1555 1555 2.34 LINK OE2 GLU A 353 ZN ZN A 502 2454 1555 2.42 LINK ND1 HIS A 457 ZN ZN A 502 1555 1555 2.19 SITE 1 AC1 4 CYS A 247 CYS A 250 CYS A 280 CYS A 283 SITE 1 AC2 4 GLU A 353 HIS A 454 HIS A 455 HIS A 457 SITE 1 AC3 4 LYS A 358 LEU A 360 LYS A 445 HIS A 456 SITE 1 AC4 13 TRP A 241 CYS A 250 GLY A 251 ASN A 274 SITE 2 AC4 13 ARG A 291 ASN A 293 ARG A 305 CYS A 306 SITE 3 AC4 13 GLY A 307 ASP A 332 HIS A 333 VAL A 334 SITE 4 AC4 13 HIS A 454 CRYST1 96.958 52.097 80.848 90.00 113.50 90.00 C 1 2 1 4 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 0.010314 0.000000 0.004485 0.00000 SCALE2 0.000000 0.019195 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013488 0.00000