HEADER HYDROLASE 23-NOV-05 2F4M 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: UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG B; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: XPCB DOMAIN, RESIDUES 273-332; COMPND 11 SYNONYM: MHR23B, XP-C REPAIR COMPLEMENTING COMPLEX 58 KDA PROTEIN, COMPND 12 P58; COMPND 13 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 KEYWDS GLYCOPROTEINS, UBIQUITIN-DEPENDENT PROTEIN DEGRADATION, NUCLEOTIDE KEYWDS 2 EXCISION REPAIR, PEPTIDE:N-GLYCANASE, TRANSGLUTAMINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.ZHAO,X.ZHOU,L.WANG,C.KISKER,W.J.LENNARZ,H.SCHINDELIN REVDAT 5 16-OCT-24 2F4M 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2F4M 1 VERSN REVDAT 3 24-FEB-09 2F4M 1 VERSN REVDAT 2 08-AUG-06 2F4M 1 JRNL REVDAT 1 07-MAR-06 2F4M 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 29636 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1579 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1474 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2953 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 42.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.55000 REMARK 3 B22 (A**2) : 1.07000 REMARK 3 B33 (A**2) : -2.43000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.155 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.672 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3023 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2685 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4086 ; 1.547 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6274 ; 0.915 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 354 ; 6.909 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;38.561 ;24.146 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 553 ;17.370 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;21.925 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 432 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3334 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 614 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 642 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2797 ; 0.196 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1377 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1684 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 178 ; 0.259 ; 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): 22 ; 0.153 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 57 ; 0.168 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.334 ; 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): 2333 ; 1.010 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 715 ; 0.249 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2881 ; 1.214 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1443 ; 2.009 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1205 ; 2.793 ; 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): 43.5334 2.1759 7.4902 REMARK 3 T TENSOR REMARK 3 T11: 0.0127 T22: -0.1252 REMARK 3 T33: -0.1705 T12: 0.0109 REMARK 3 T13: 0.1361 T23: -0.0270 REMARK 3 L TENSOR REMARK 3 L11: 8.6948 L22: 5.4009 REMARK 3 L33: 7.1510 L12: 1.0772 REMARK 3 L13: -4.7860 L23: -0.6303 REMARK 3 S TENSOR REMARK 3 S11: -0.4700 S12: 0.2366 S13: -0.7672 REMARK 3 S21: -0.2132 S22: -0.0814 S23: -0.4445 REMARK 3 S31: 1.0602 S32: 0.2178 S33: 0.5514 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): 27.8185 19.4806 19.2027 REMARK 3 T TENSOR REMARK 3 T11: -0.1602 T22: -0.2330 REMARK 3 T33: -0.2395 T12: 0.0282 REMARK 3 T13: 0.0012 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 3.7935 L22: 3.2683 REMARK 3 L33: 5.2196 L12: -0.7945 REMARK 3 L13: -1.8505 L23: 0.0078 REMARK 3 S TENSOR REMARK 3 S11: 0.2154 S12: 0.2474 S13: 0.5588 REMARK 3 S21: -0.1751 S22: 0.0066 S23: 0.0275 REMARK 3 S31: -0.6417 S32: -0.3520 S33: -0.2220 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 501 REMARK 3 ORIGIN FOR THE GROUP (A): 4.0347 21.2685 37.6400 REMARK 3 T TENSOR REMARK 3 T11: -0.1532 T22: 0.0753 REMARK 3 T33: -0.0159 T12: 0.1096 REMARK 3 T13: 0.0100 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 9.4823 L22: 4.4019 REMARK 3 L33: 21.1726 L12: -3.5453 REMARK 3 L13: -8.6058 L23: 3.2967 REMARK 3 S TENSOR REMARK 3 S11: -0.2549 S12: 0.7513 S13: -0.5820 REMARK 3 S21: -0.0593 S22: 0.0263 S23: 0.4918 REMARK 3 S31: 0.5479 S32: -0.7278 S33: 0.2285 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 2F4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 5 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 : 31216 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 20.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.40000 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 8.5, 28-32% REMARK 280 PEG4000, 0.2 M SODIUM ACETATE, 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 49.11250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.14850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.11250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.14850 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 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: 1920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 62.90839 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 74.61172 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 HOH B 170 O HOH B 257 1.38 REMARK 500 O HOH A 513 O HOH A 677 1.53 REMARK 500 O ILE A 195 O HOH A 665 2.03 REMARK 500 O HOH B 218 O HOH B 257 2.04 REMARK 500 NE ARG A 408 O HOH A 688 2.05 REMARK 500 O LEU A 192 O HOH A 665 2.07 REMARK 500 O HOH A 530 O HOH A 600 2.07 REMARK 500 O GLN B 315 NE2 GLN B 319 2.16 REMARK 500 O HOH A 575 O HOH A 602 2.16 REMARK 500 OD1 ASN A 412 O HOH A 683 2.17 REMARK 500 O HOH A 566 O HOH A 611 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 573 O HOH A 696 4555 2.01 REMARK 500 O HOH A 708 O HOH A 715 4546 2.06 REMARK 500 OE1 GLU A 353 O HOH A 530 2656 2.12 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 219 -111.66 54.43 REMARK 500 VAL A 220 -79.95 -152.90 REMARK 500 SER A 221 124.83 79.54 REMARK 500 ASP A 222 -65.34 -162.11 REMARK 500 ASN A 243 -73.02 -101.50 REMARK 500 PRO A 263 81.58 -56.37 REMARK 500 ASN A 264 -65.29 -19.92 REMARK 500 ASP A 265 -46.78 178.36 REMARK 500 ARG A 305 -159.97 -108.23 REMARK 500 TRP A 335 -159.57 -155.77 REMARK 500 SER A 371 -65.50 -132.39 REMARK 500 LEU A 451 -50.07 -130.33 REMARK 500 HIS B 274 -145.47 -106.09 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 106.2 REMARK 620 3 CYS A 280 SG 108.3 112.2 REMARK 620 4 CYS A 283 SG 110.2 107.4 112.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2F4O RELATED DB: PDB REMARK 900 THE MOUSE PNGASE-HR23 COMPLEX IN COMPLEX WITH AN INHIBITOR DBREF 2F4M A 164 450 UNP Q9JI78 Q9JI78_MOUSE 164 450 DBREF 2F4M B 273 332 UNP P54728 RD23B_MOUSE 273 332 SEQADV 2F4M LEU A 451 UNP Q9JI78 CLONING ARTIFACT SEQADV 2F4M GLU A 452 UNP Q9JI78 CLONING ARTIFACT SEQADV 2F4M HIS A 453 UNP Q9JI78 EXPRESSION TAG SEQADV 2F4M HIS A 454 UNP Q9JI78 EXPRESSION TAG SEQADV 2F4M HIS A 455 UNP Q9JI78 EXPRESSION TAG SEQADV 2F4M HIS A 456 UNP Q9JI78 EXPRESSION TAG SEQADV 2F4M HIS A 457 UNP Q9JI78 EXPRESSION TAG SEQADV 2F4M HIS A 458 UNP Q9JI78 EXPRESSION TAG SEQADV 2F4M 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 HET ZN A 501 1 HET CL A 1 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 3 ZN ZN 2+ FORMUL 4 CL CL 1- FORMUL 5 HOH *255(H2 O) HELIX 1 1 SER A 166 LEU A 181 1 16 HELIX 2 2 ASN A 184 ILE A 195 1 12 HELIX 3 3 PRO A 196 ARG A 212 1 17 HELIX 4 4 ASP A 222 GLU A 237 1 16 HELIX 5 5 ASP A 265 TRP A 270 1 6 HELIX 6 6 ASN A 294 ARG A 302 1 9 HELIX 7 7 ARG A 305 LEU A 320 1 16 HELIX 8 8 LYS A 358 TYR A 362 5 5 HELIX 9 9 THR A 385 SER A 389 5 5 HELIX 10 10 LYS A 391 ARG A 399 1 9 HELIX 11 11 LYS A 403 LEU A 420 1 18 HELIX 12 12 SER A 423 ILE A 442 1 20 HELIX 13 13 HIS B 274 ARG B 280 5 7 HELIX 14 14 GLN B 282 ASN B 295 1 14 HELIX 15 15 LEU B 298 ASN B 310 1 13 HELIX 16 16 ASN B 310 HIS B 320 1 11 HELIX 17 17 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 SER A 256 0 SHEET 2 B 3 VAL A 275 CYS A 280 -1 O TYR A 279 N ARG A 255 SHEET 3 B 3 LEU A 285 PRO A 290 -1 O LEU A 285 N CYS A 280 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 SER A 340 O ARG A 345 SHEET 4 C 6 ALA A 324 ASP A 329 -1 N VAL A 327 O TRP A 335 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 SSBOND 1 CYS A 306 CYS A 352 1555 1555 2.07 LINK SG CYS A 247 ZN ZN A 501 1555 1555 2.41 LINK SG CYS A 250 ZN ZN A 501 1555 1555 2.29 LINK SG CYS A 280 ZN ZN A 501 1555 1555 2.29 LINK SG CYS A 283 ZN ZN A 501 1555 1555 2.42 SITE 1 AC1 4 CYS A 247 CYS A 250 CYS A 280 CYS A 283 SITE 1 AC2 6 LYS A 358 PRO A 359 LEU A 360 LYS A 445 SITE 2 AC2 6 HIS A 454 HIS A 455 CRYST1 98.225 52.297 82.548 90.00 115.33 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 0.010181 0.000000 0.004819 0.00000 SCALE2 0.000000 0.019122 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013403 0.00000