HEADER HYDROLASE 28-MAR-14 4PYZ TITLE CRYSTAL STRUCTURE OF THE FIRST TWO UBL DOMAINS OF DEUBIQUITYLASE USP7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 537-793; COMPND 5 SYNONYM: DEUBIQUITINATING ENZYME 7, HERPESVIRUS-ASSOCIATED UBIQUITIN- COMPND 6 SPECIFIC PROTEASE, UBIQUITIN THIOESTERASE 7, UBIQUITIN-SPECIFIC- COMPND 7 PROCESSING PROTEASE 7; COMPND 8 EC: 3.4.19.12; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP7, HAUSP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V2R; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-LIC KEYWDS DEUBIQUITYLASE, UBIQUITIN-LIKE DOMAIN, STRUCTURAL GENOMICS, KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, SGC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.R.WALKER,A.DONG,M.S.ONG,S.DHE-PAGANON,J.KANIA,C.BOUNTRA, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,Y.TONG,STRUCTURAL GENOMICS CONSORTIUM AUTHOR 3 (SGC) REVDAT 3 20-SEP-23 4PYZ 1 SEQADV REVDAT 2 22-NOV-17 4PYZ 1 REMARK REVDAT 1 16-APR-14 4PYZ 0 JRNL AUTH M.S.ONG,J.R.WALKER,A.DONG,S.DHE-PAGANON,J.KANIA,C.BOUNTRA, JRNL AUTH 2 C.H.ARROWSMITH,A.M.EDWARDS,Y.TONG, JRNL AUTH 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL CRYSTAL STRUCTURE OF THE FIRST TWO UBL DOMAINS OF JRNL TITL 2 DEUBIQUITYLASE USP7 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 19769 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.180 REMARK 3 FREE R VALUE TEST SET COUNT : 629 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.84 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.34 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2659 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.3211 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2585 REMARK 3 BIN R VALUE (WORKING SET) : 0.3198 REMARK 3 BIN FREE R VALUE : 0.3722 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 2.78 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 74 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4062 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 82.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 37.23320 REMARK 3 B22 (A**2) : 5.63840 REMARK 3 B33 (A**2) : -42.87160 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.564 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.768 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.874 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4179 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5682 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1441 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 127 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 606 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4179 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 555 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4427 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.91 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.82 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.54 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|531 - A|793 } REMARK 3 ORIGIN FOR THE GROUP (A): 21.2636 -20.5670 -20.3683 REMARK 3 T TENSOR REMARK 3 T11: 0.0918 T22: 0.1879 REMARK 3 T33: 0.1910 T12: -0.0712 REMARK 3 T13: 0.0409 T23: -0.0425 REMARK 3 L TENSOR REMARK 3 L11: 1.3183 L22: 1.2423 REMARK 3 L33: 0.6303 L12: -0.2050 REMARK 3 L13: 0.0260 L23: -0.3117 REMARK 3 S TENSOR REMARK 3 S11: -0.0707 S12: 0.3199 S13: -0.1038 REMARK 3 S21: -0.1195 S22: -0.0010 S23: -0.0973 REMARK 3 S31: 0.2187 S32: 0.0130 S33: 0.0717 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|533 - B|793 } REMARK 3 ORIGIN FOR THE GROUP (A): 44.1291 -11.2558 -16.5863 REMARK 3 T TENSOR REMARK 3 T11: 0.0680 T22: 0.0268 REMARK 3 T33: 0.2493 T12: -0.0485 REMARK 3 T13: -0.0825 T23: 0.1079 REMARK 3 L TENSOR REMARK 3 L11: 1.3112 L22: 0.8257 REMARK 3 L33: 1.1883 L12: -0.1888 REMARK 3 L13: -0.2238 L23: 0.5161 REMARK 3 S TENSOR REMARK 3 S11: -0.0578 S12: 0.0949 S13: 0.3104 REMARK 3 S21: -0.0378 S22: 0.0616 S23: 0.0160 REMARK 3 S31: -0.1803 S32: 0.0028 S33: -0.0038 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4PYZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085395. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97924 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19822 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.830 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.93600 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2YLM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 4000, 0.2 M NH4AC, 0.1 M REMARK 280 NACITRATE PH5.6, VAPOR DIFFUSION HANGING DROP, TEMPERATURE 291K, REMARK 280 VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 34.16400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.09850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.87750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.09850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.16400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.87750 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: AS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 SER A 521 REMARK 465 HIS A 522 REMARK 465 HIS A 523 REMARK 465 HIS A 524 REMARK 465 HIS A 525 REMARK 465 HIS A 526 REMARK 465 HIS A 527 REMARK 465 SER A 528 REMARK 465 SER A 529 REMARK 465 GLY A 530 REMARK 465 SER B 521 REMARK 465 HIS B 522 REMARK 465 HIS B 523 REMARK 465 HIS B 524 REMARK 465 HIS B 525 REMARK 465 HIS B 526 REMARK 465 HIS B 527 REMARK 465 SER B 528 REMARK 465 SER B 529 REMARK 465 GLY B 530 REMARK 465 LEU B 531 REMARK 465 VAL B 532 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 546 CG CD OE1 OE2 REMARK 470 GLU A 547 CD OE1 OE2 REMARK 470 LYS A 548 CE NZ REMARK 470 ARG A 549 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 553 CG CD OE1 NE2 REMARK 470 LYS A 554 CD CE NZ REMARK 470 LYS A 556 CD CE NZ REMARK 470 GLU A 587 CD OE1 OE2 REMARK 470 LYS A 588 CD CE NZ REMARK 470 LYS A 595 CD CE NZ REMARK 470 LEU A 597 CG CD1 CD2 REMARK 470 GLN A 611 CG CD OE1 NE2 REMARK 470 MET A 613 CG SD CE REMARK 470 ASN A 640 CG OD1 ND2 REMARK 470 GLU A 641 CG CD OE1 OE2 REMARK 470 ASP A 666 CG OD1 OD2 REMARK 470 GLU A 668 OE1 OE2 REMARK 470 THR A 675 OG1 CG2 REMARK 470 LYS A 678 CG CD CE NZ REMARK 470 LYS A 681 CG CD CE NZ REMARK 470 LYS A 695 CE NZ REMARK 470 LYS A 712 CG CD CE NZ REMARK 470 LEU A 753 CD1 CD2 REMARK 470 LYS A 755 CG CD CE NZ REMARK 470 GLU A 759 CD OE1 OE2 REMARK 470 ARG A 788 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 543 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 547 CG CD OE1 OE2 REMARK 470 LYS B 548 CD CE NZ REMARK 470 ILE B 550 CG1 CG2 CD1 REMARK 470 LYS B 554 CD CE NZ REMARK 470 LYS B 556 CG CD CE NZ REMARK 470 GLU B 587 CG CD OE1 OE2 REMARK 470 LYS B 588 CG CD CE NZ REMARK 470 LYS B 595 CE NZ REMARK 470 GLN B 611 OE1 NE2 REMARK 470 GLN B 619 CG CD OE1 NE2 REMARK 470 ARG B 621 NE CZ NH1 NH2 REMARK 470 SER B 629 OG REMARK 470 GLU B 641 CG CD OE1 OE2 REMARK 470 ASN B 645 CG OD1 ND2 REMARK 470 LYS B 646 CG CD CE NZ REMARK 470 ASP B 666 CG OD1 OD2 REMARK 470 LEU B 669 CG CD1 CD2 REMARK 470 SER B 672 OG REMARK 470 LYS B 678 CG CD CE NZ REMARK 470 LYS B 681 CG CD CE NZ REMARK 470 HIS B 683 CG ND1 CD2 CE1 NE2 REMARK 470 LEU B 687 CD1 CD2 REMARK 470 LYS B 695 CG CD CE NZ REMARK 470 SER B 710 OG REMARK 470 GLN B 728 CG CD OE1 NE2 REMARK 470 ASP B 729 CG OD1 OD2 REMARK 470 GLU B 744 CD OE1 OE2 REMARK 470 LEU B 753 CG CD1 CD2 REMARK 470 LYS B 755 CG CD CE NZ REMARK 470 GLU B 759 CD OE1 OE2 REMARK 470 LYS B 770 CD CE NZ REMARK 470 GLU B 774 CG CD OE1 OE2 REMARK 470 ASN B 777 CG OD1 ND2 REMARK 470 GLU B 785 OE1 OE2 REMARK 470 ARG B 788 CG CD NE CZ NH1 NH2 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 ASP A 582 -165.27 67.92 REMARK 500 ASN A 741 -12.92 86.18 REMARK 500 ASP B 582 -158.86 66.45 REMARK 500 ASP B 729 68.73 63.62 REMARK 500 ASN B 741 -7.36 83.73 REMARK 500 HIS B 792 30.72 -90.05 REMARK 500 REMARK 500 REMARK: NULL DBREF 4PYZ A 537 793 UNP Q93009 UBP7_HUMAN 537 793 DBREF 4PYZ B 537 793 UNP Q93009 UBP7_HUMAN 537 793 SEQADV 4PYZ SER A 521 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS A 522 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS A 523 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS A 524 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS A 525 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS A 526 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS A 527 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ SER A 528 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ SER A 529 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ GLY A 530 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ LEU A 531 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ VAL A 532 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ PRO A 533 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ ARG A 534 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ GLY A 535 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ SER A 536 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ SER B 521 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS B 522 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS B 523 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS B 524 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS B 525 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS B 526 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ HIS B 527 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ SER B 528 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ SER B 529 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ GLY B 530 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ LEU B 531 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ VAL B 532 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ PRO B 533 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ ARG B 534 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ GLY B 535 UNP Q93009 EXPRESSION TAG SEQADV 4PYZ SER B 536 UNP Q93009 EXPRESSION TAG SEQRES 1 A 273 SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO SEQRES 2 A 273 ARG GLY SER PRO GLN GLN LEU VAL GLU ARG LEU GLN GLU SEQRES 3 A 273 GLU LYS ARG ILE GLU ALA GLN LYS ARG LYS GLU ARG GLN SEQRES 4 A 273 GLU ALA HIS LEU TYR MET GLN VAL GLN ILE VAL ALA GLU SEQRES 5 A 273 ASP GLN PHE CYS GLY HIS GLN GLY ASN ASP MET TYR ASP SEQRES 6 A 273 GLU GLU LYS VAL LYS TYR THR VAL PHE LYS VAL LEU LYS SEQRES 7 A 273 ASN SER SER LEU ALA GLU PHE VAL GLN SER LEU SER GLN SEQRES 8 A 273 THR MET GLY PHE PRO GLN ASP GLN ILE ARG LEU TRP PRO SEQRES 9 A 273 MET GLN ALA ARG SER ASN GLY THR LYS ARG PRO ALA MET SEQRES 10 A 273 LEU ASP ASN GLU ALA ASP GLY ASN LYS THR MET ILE GLU SEQRES 11 A 273 LEU SER ASP ASN GLU ASN PRO TRP THR ILE PHE LEU GLU SEQRES 12 A 273 THR VAL ASP PRO GLU LEU ALA ALA SER GLY ALA THR LEU SEQRES 13 A 273 PRO LYS PHE ASP LYS ASP HIS ASP VAL MET LEU PHE LEU SEQRES 14 A 273 LYS MET TYR ASP PRO LYS THR ARG SER LEU ASN TYR CYS SEQRES 15 A 273 GLY HIS ILE TYR THR PRO ILE SER CYS LYS ILE ARG ASP SEQRES 16 A 273 LEU LEU PRO VAL MET CYS ASP ARG ALA GLY PHE ILE GLN SEQRES 17 A 273 ASP THR SER LEU ILE LEU TYR GLU GLU VAL LYS PRO ASN SEQRES 18 A 273 LEU THR GLU ARG ILE GLN ASP TYR ASP VAL SER LEU ASP SEQRES 19 A 273 LYS ALA LEU ASP GLU LEU MET ASP GLY ASP ILE ILE VAL SEQRES 20 A 273 PHE GLN LYS ASP ASP PRO GLU ASN ASP ASN SER GLU LEU SEQRES 21 A 273 PRO THR ALA LYS GLU TYR PHE ARG ASP LEU TYR HIS ARG SEQRES 1 B 273 SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO SEQRES 2 B 273 ARG GLY SER PRO GLN GLN LEU VAL GLU ARG LEU GLN GLU SEQRES 3 B 273 GLU LYS ARG ILE GLU ALA GLN LYS ARG LYS GLU ARG GLN SEQRES 4 B 273 GLU ALA HIS LEU TYR MET GLN VAL GLN ILE VAL ALA GLU SEQRES 5 B 273 ASP GLN PHE CYS GLY HIS GLN GLY ASN ASP MET TYR ASP SEQRES 6 B 273 GLU GLU LYS VAL LYS TYR THR VAL PHE LYS VAL LEU LYS SEQRES 7 B 273 ASN SER SER LEU ALA GLU PHE VAL GLN SER LEU SER GLN SEQRES 8 B 273 THR MET GLY PHE PRO GLN ASP GLN ILE ARG LEU TRP PRO SEQRES 9 B 273 MET GLN ALA ARG SER ASN GLY THR LYS ARG PRO ALA MET SEQRES 10 B 273 LEU ASP ASN GLU ALA ASP GLY ASN LYS THR MET ILE GLU SEQRES 11 B 273 LEU SER ASP ASN GLU ASN PRO TRP THR ILE PHE LEU GLU SEQRES 12 B 273 THR VAL ASP PRO GLU LEU ALA ALA SER GLY ALA THR LEU SEQRES 13 B 273 PRO LYS PHE ASP LYS ASP HIS ASP VAL MET LEU PHE LEU SEQRES 14 B 273 LYS MET TYR ASP PRO LYS THR ARG SER LEU ASN TYR CYS SEQRES 15 B 273 GLY HIS ILE TYR THR PRO ILE SER CYS LYS ILE ARG ASP SEQRES 16 B 273 LEU LEU PRO VAL MET CYS ASP ARG ALA GLY PHE ILE GLN SEQRES 17 B 273 ASP THR SER LEU ILE LEU TYR GLU GLU VAL LYS PRO ASN SEQRES 18 B 273 LEU THR GLU ARG ILE GLN ASP TYR ASP VAL SER LEU ASP SEQRES 19 B 273 LYS ALA LEU ASP GLU LEU MET ASP GLY ASP ILE ILE VAL SEQRES 20 B 273 PHE GLN LYS ASP ASP PRO GLU ASN ASP ASN SER GLU LEU SEQRES 21 B 273 PRO THR ALA LYS GLU TYR PHE ARG ASP LEU TYR HIS ARG HET UNX B1000 1 HET UNX B1001 1 HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 UNX 2(X) FORMUL 5 HOH *12(H2 O) HELIX 1 1 SER A 536 GLU A 560 1 25 HELIX 2 2 ASP A 573 PHE A 575 5 3 HELIX 3 3 SER A 601 GLY A 614 1 14 HELIX 4 4 PRO A 616 ASP A 618 5 3 HELIX 5 5 THR A 647 ASP A 653 1 7 HELIX 6 6 ASP A 666 SER A 672 1 7 HELIX 7 7 ILE A 713 ASP A 715 5 3 HELIX 8 8 LEU A 716 GLY A 725 1 10 HELIX 9 9 SER A 752 LEU A 757 1 6 HELIX 10 10 ASP A 772 SER A 778 5 7 HELIX 11 11 THR A 782 HIS A 792 1 11 HELIX 12 12 SER B 536 ALA B 561 1 26 HELIX 13 13 ASP B 573 PHE B 575 5 3 HELIX 14 14 SER B 601 GLY B 614 1 14 HELIX 15 15 PRO B 616 ASP B 618 5 3 HELIX 16 16 THR B 647 ASP B 653 1 7 HELIX 17 17 LEU B 716 GLY B 725 1 10 HELIX 18 18 SER B 752 LEU B 757 1 6 HELIX 19 19 ASP B 772 SER B 778 5 7 HELIX 20 20 THR B 782 HIS B 792 1 11 SHEET 1 A 5 THR A 592 LEU A 597 0 SHEET 2 A 5 TYR A 564 ALA A 571 -1 N MET A 565 O VAL A 596 SHEET 3 A 5 TRP A 658 THR A 664 1 O TRP A 658 N GLN A 568 SHEET 4 A 5 ILE A 620 ALA A 627 -1 N TRP A 623 O PHE A 661 SHEET 5 A 5 LYS A 633 PRO A 635 -1 O ARG A 634 N GLN A 626 SHEET 1 B 5 SER A 698 PRO A 708 0 SHEET 2 B 5 ASP A 684 ASP A 693 -1 N MET A 691 O ASN A 700 SHEET 3 B 5 ILE A 765 LYS A 770 1 O PHE A 768 N TYR A 692 SHEET 4 B 5 LEU A 732 LYS A 739 -1 N TYR A 735 O VAL A 767 SHEET 5 B 5 LEU A 742 ARG A 745 -1 O LEU A 742 N LYS A 739 SHEET 1 C 5 THR B 592 LEU B 597 0 SHEET 2 C 5 TYR B 564 ALA B 571 -1 N MET B 565 O VAL B 596 SHEET 3 C 5 TRP B 658 THR B 664 1 O LEU B 662 N VAL B 570 SHEET 4 C 5 ILE B 620 ALA B 627 -1 N TRP B 623 O PHE B 661 SHEET 5 C 5 LYS B 633 PRO B 635 -1 O ARG B 634 N GLN B 626 SHEET 1 D 5 SER B 698 PRO B 708 0 SHEET 2 D 5 ASP B 684 ASP B 693 -1 N LEU B 689 O GLY B 703 SHEET 3 D 5 ASP B 764 LYS B 770 1 O ASP B 764 N PHE B 688 SHEET 4 D 5 LEU B 732 LYS B 739 -1 N ILE B 733 O GLN B 769 SHEET 5 D 5 LEU B 742 ARG B 745 -1 O GLU B 744 N GLU B 736 SSBOND 1 CYS A 576 CYS B 576 1555 1555 2.04 CISPEP 1 ASN A 656 PRO A 657 0 2.75 CISPEP 2 ASN B 656 PRO B 657 0 2.29 CRYST1 68.328 103.755 116.197 90.00 90.00 90.00 P 21 21 21 8 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 0.014635 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009638 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008606 0.00000