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PDBsum entry 2len

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Hydrolase PDB id
2len
Jmol
Contents
Protein chain
231 a.a.
HEADER    HYDROLASE                               19-JUN-11   2LEN
TITLE     SOLUTION STRUCTURE OF UCHL1 S18Y VARIANT
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L1;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: UCH-L1, NEURON CYTOPLASMIC PROTEIN 9.5, PGP 9.5, PGP9.5,
COMPND   5 UBIQUITIN THIOESTERASE L1;
COMPND   6 EC: 3.4.19.12;
COMPND   7 ENGINEERED: YES;
COMPND   8 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: UCHL1;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: ROSETTA BL21;
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;
SOURCE  10 EXPRESSION_SYSTEM_VECTOR: PET22B
KEYWDS    HYDROLASE
EXPDTA    SOLUTION NMR
NUMMDL    20
MDLTYP    MINIMIZED AVERAGE
AUTHOR    H.TSE
REVDAT   1   20-JUN-12 2LEN    0
JRNL        AUTH   H.TSE,K.SZE,H.HU
JRNL        TITL   BACKBONE AND SIDE-CHAIN (1)H, (15)N AND (13)C RESONANCE
JRNL        TITL 2 ASSIGNMENTS OF S18Y MUTANT OF UBIQUITIN CARBOXY-TERMINAL
JRNL        TITL 3 HYDROLASE L1
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   2
REMARK   2 RESOLUTION. NOT APPLICABLE.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : AMBER
REMARK   3   AUTHORS     : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG,
REMARK   3                 DUKE, LUO, ... AND KOLLM
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 2LEN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-11.
REMARK 100 THE RCSB ID CODE IS RCSB102300.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210  EXPERIMENT TYPE                : NMR
REMARK 210  TEMPERATURE           (KELVIN) : 298
REMARK 210  PH                             : 6.5
REMARK 210  IONIC STRENGTH                 : 100
REMARK 210  PRESSURE                       : AMBIENT
REMARK 210  SAMPLE CONTENTS                : 0.7-0.8MM [U-99% 13C; U-99% 15N]
REMARK 210                                   UCHL1 S18Y VARIANT-1, 20MM SODIUM
REMARK 210                                   PHOSPHATE-2, 100MM SODIUM
REMARK 210                                   CHLORIDE-3, 3MM DTT-4, 90% H2O-5,
REMARK 210                                   10% D2O-6, 90% H2O/10% D2O
REMARK 210
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 2D 1H-13C HSQC;
REMARK 210                                   3D CBCA(CO)NH; 3D HNCO; 3D HNCA;
REMARK 210                                   3D HNCACB; 3D HBHA(CO)NH; 3D
REMARK 210                                   HN(CO)CA; 3D HCCH-TOCSY; 3D
REMARK 210                                   HN(CA)CO; 3D HCCH-COSY; 3D 1H-15N
REMARK 210                                   NOESY; 3D 1H-13C NOESY ALIPHATIC;
REMARK 210                                   3D 1H-13C NOESY AROMATIC; 3D 1H-
REMARK 210                                   15N TOCSY
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ
REMARK 210  SPECTROMETER MODEL             : AVANCE
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER
REMARK 210
REMARK 210  STRUCTURE DETERMINATION.
REMARK 210   SOFTWARE USED                 : XWINNMR, SPARKY, CYANA, TALOS
REMARK 210   METHOD USED                   : MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 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: MONOMERIC
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 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 12 ARG A  63   NE  -  CZ  -  NH1 ANGL. DEV. =   3.2 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  1 LYS A  71       48.37     39.77
REMARK 500  1 MET A  82     -163.23   -128.46
REMARK 500  1 LYS A  83      -50.67   -123.34
REMARK 500  1 SER A  89       87.82    -69.96
REMARK 500  1 ASP A 110       98.96    -57.28
REMARK 500  1 SER A 112       90.56    -68.68
REMARK 500  1 ASN A 159      -70.45   -128.49
REMARK 500  1 ASP A 169       16.21     56.39
REMARK 500  1 GLU A 211       13.59    -67.61
REMARK 500  2 ILE A   8      102.49    -57.37
REMARK 500  2 GLU A 137      -65.95   -123.49
REMARK 500  2 ASP A 169       17.28     55.77
REMARK 500  2 GLU A 211       15.96    -67.49
REMARK 500  2 HIS A 228       50.54   -145.13
REMARK 500  3 PRO A   5       99.18    -68.49
REMARK 500  3 ASN A  88       28.96    -74.29
REMARK 500  3 SER A  89       85.52    -65.12
REMARK 500  3 SER A 112       93.40    -62.01
REMARK 500  3 GLU A 137      -63.86   -131.42
REMARK 500  3 ASP A 169       15.92     56.53
REMARK 500  3 LEU A 175       64.79   -107.69
REMARK 500  3 PRO A 180       49.82    -78.71
REMARK 500  3 ALA A 222      -96.23    -84.32
REMARK 500  4 CYS A  90       95.20    -59.94
REMARK 500  4 SER A 112       85.95    -66.61
REMARK 500  4 GLU A 137      -62.49    -91.10
REMARK 500  4 ASP A 169       18.76     54.13
REMARK 500  4 PRO A 180       26.89    -76.46
REMARK 500  5 SER A  89       97.82    -53.13
REMARK 500  5 SER A 112      103.83    -59.35
REMARK 500  5 GLU A 137      -60.26   -103.98
REMARK 500  5 LEU A 175       70.01   -115.42
REMARK 500  5 GLU A 211       78.53     58.96
REMARK 500  5 HIS A 226       95.93    -64.85
REMARK 500  6 ASN A  88       27.18    -73.18
REMARK 500  6 SER A  89       90.43    -61.81
REMARK 500  6 LEU A 106       96.40    -65.90
REMARK 500  6 GLU A 137      -56.98   -128.05
REMARK 500  6 ASP A 169       13.13     59.16
REMARK 500  6 ASN A 184       99.35    -67.46
REMARK 500  7 LEU A 106       90.35    -68.70
REMARK 500  7 SER A 112       96.59    -67.58
REMARK 500  7 MET A 124     -109.04    -93.08
REMARK 500  7 GLU A 137      -55.78   -131.75
REMARK 500  7 ARG A 213       70.83     38.52
REMARK 500  7 ALA A 223      108.84    -60.00
REMARK 500  8 ASP A 110       96.96    -65.02
REMARK 500  8 GLU A 137      -70.78   -112.41
REMARK 500  8 ASP A 169       18.91     55.38
REMARK 500  8 VAL A 212     -169.94   -128.65
REMARK 500
REMARK 500 THIS ENTRY HAS     129 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500  M RES CSSEQI        RMS     TYPE
REMARK 500 19 ARG A 129         0.09    SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3IFW   RELATED DB: PDB
REMARK 900 RELATED ID: 3KVF   RELATED DB: PDB
REMARK 900 RELATED ID: 3KW5   RELATED DB: PDB
REMARK 900 RELATED ID: 3IRT   RELATED DB: PDB
REMARK 900 RELATED ID: 2ETL   RELATED DB: PDB
REMARK 900 RELATED ID: 17260   RELATED DB: BMRB
DBREF  2LEN A    1   223  UNP    P09936   UCHL1_HUMAN      1    223
SEQADV 2LEN TYR A   18  UNP  P09936    SER    18 ENGINEERED MUTATION
SEQADV 2LEN LEU A  224  UNP  P09936              EXPRESSION TAG
SEQADV 2LEN GLU A  225  UNP  P09936              EXPRESSION TAG
SEQADV 2LEN HIS A  226  UNP  P09936              EXPRESSION TAG
SEQADV 2LEN HIS A  227  UNP  P09936              EXPRESSION TAG
SEQADV 2LEN HIS A  228  UNP  P09936              EXPRESSION TAG
SEQADV 2LEN HIS A  229  UNP  P09936              EXPRESSION TAG
SEQADV 2LEN HIS A  230  UNP  P09936              EXPRESSION TAG
SEQADV 2LEN HIS A  231  UNP  P09936              EXPRESSION TAG
SEQRES   1 A  231  MET GLN LEU LYS PRO MET GLU ILE ASN PRO GLU MET LEU
SEQRES   2 A  231  ASN LYS VAL LEU TYR ARG LEU GLY VAL ALA GLY GLN TRP
SEQRES   3 A  231  ARG PHE VAL ASP VAL LEU GLY LEU GLU GLU GLU SER LEU
SEQRES   4 A  231  GLY SER VAL PRO ALA PRO ALA CYS ALA LEU LEU LEU LEU
SEQRES   5 A  231  PHE PRO LEU THR ALA GLN HIS GLU ASN PHE ARG LYS LYS
SEQRES   6 A  231  GLN ILE GLU GLU LEU LYS GLY GLN GLU VAL SER PRO LYS
SEQRES   7 A  231  VAL TYR PHE MET LYS GLN THR ILE GLY ASN SER CYS GLY
SEQRES   8 A  231  THR ILE GLY LEU ILE HIS ALA VAL ALA ASN ASN GLN ASP
SEQRES   9 A  231  LYS LEU GLY PHE GLU ASP GLY SER VAL LEU LYS GLN PHE
SEQRES  10 A  231  LEU SER GLU THR GLU LYS MET SER PRO GLU ASP ARG ALA
SEQRES  11 A  231  LYS CYS PHE GLU LYS ASN GLU ALA ILE GLN ALA ALA HIS
SEQRES  12 A  231  ASP ALA VAL ALA GLN GLU GLY GLN CYS ARG VAL ASP ASP
SEQRES  13 A  231  LYS VAL ASN PHE HIS PHE ILE LEU PHE ASN ASN VAL ASP
SEQRES  14 A  231  GLY HIS LEU TYR GLU LEU ASP GLY ARG MET PRO PHE PRO
SEQRES  15 A  231  VAL ASN HIS GLY ALA SER SER GLU ASP THR LEU LEU LYS
SEQRES  16 A  231  ASP ALA ALA LYS VAL CYS ARG GLU PHE THR GLU ARG GLU
SEQRES  17 A  231  GLN GLY GLU VAL ARG PHE SER ALA VAL ALA LEU CYS LYS
SEQRES  18 A  231  ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS
HELIX    1   1 ASN A    9  LEU A   20  1                                  12
HELIX    2   2 GLU A   35  GLY A   40  1                                   6
HELIX    3   3 THR A   56  LEU A   70  1                                  15
HELIX    4   4 GLY A   91  ASN A  102  1                                  12
HELIX    5   5 SER A  112  GLU A  122  1                                  11
HELIX    6   6 SER A  125  GLU A  134  1                                  10
HELIX    7   7 GLU A  137  GLY A  150  1                                  14
HELIX    8   8 SER A  189  ASP A  191  5                                   3
HELIX    9   9 THR A  192  GLU A  208  1                                  17
HELIX   10  10 GLY A  210  PHE A  214  5                                   5
SHEET    1   A 6 TRP A  26  VAL A  29  0
SHEET    2   A 6 SER A 215  LYS A 221 -1  O  ALA A 218   N  VAL A  29
SHEET    3   A 6 CYS A  47  PHE A  53 -1  N  LEU A  50   O  VAL A 217
SHEET    4   A 6 HIS A 161  VAL A 168 -1  O  PHE A 165   N  LEU A  49
SHEET    5   A 6 HIS A 171  ASP A 176 -1  O  TYR A 173   N  ASN A 166
SHEET    6   A 6 VAL A 183  ASN A 184 -1  O  VAL A 183   N  GLU A 174
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1
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      1.000000  0.000000  0.000000        0.00000
SCALE2      0.000000  1.000000  0.000000        0.00000
SCALE3      0.000000  0.000000  1.000000        0.00000
      
PROCHECK
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 References