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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
