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- PDB-4rxx: Crystal Structure of the N-terminal Domain of Human Ubiquitin Spe... -

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Basic information

Entry
Database: PDB / ID: 4rxx
TitleCrystal Structure of the N-terminal Domain of Human Ubiquitin Specific Protease 38
ComponentsUbiquitin carboxyl-terminal hydrolase 38
KeywordsHYDROLASE / Ubiquitin-specific protease / heat-repeat / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein deubiquitination / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cysteine-type endopeptidase activity / nucleus / cytosol
Similarity search - Function
Ubiquitin-specific peptidase 38 / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 38
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.06 Å
AuthorsDong, A. / Shen, L. / Hu, J. / Li, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure of the N-terminal Domain of Human Ubiquitin Specific Protease 38
Authors: Shen, L. / Dong, A. / Hu, J. / Li, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y.
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6628
Polymers49,5651
Non-polymers987
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.985, 102.039, 135.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 38 / Deubiquitinating enzyme 38 / HP43.8KD / Ubiquitin thioesterase 38 / Ubiquitin-specific-processing protease 38


Mass: 49564.949 Da / Num. of mol.: 1 / Fragment: N-terminal Domain (UNP residues 1-424)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP38, KIAA1891 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R pRARE2 / References: UniProt: Q8NB14, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein sample was first mixed Hampton Research Additive Screen H03 40% in 10:1 (V/V) Protein:1,3-propanediol ratio, then set up with 15% PEG8000, 0.2 M MgCl2, 0.1 M HEPES, pH 7.5, vapor ...Details: Protein sample was first mixed Hampton Research Additive Screen H03 40% in 10:1 (V/V) Protein:1,3-propanediol ratio, then set up with 15% PEG8000, 0.2 M MgCl2, 0.1 M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 37072 / % possible obs: 99.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.127 / Χ2: 1.463 / Net I/σ(I): 22.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.06-2.15.90.8217970.625197.3
2.1-2.136.80.73717910.674199.2
2.13-2.1780.73518070.6451100
2.17-2.229.10.67918680.671100
2.22-2.279.50.59317910.7071100
2.27-2.329.90.53518420.7191100
2.32-2.3810.20.44618220.7531100
2.38-2.4410.50.4118080.771100
2.44-2.5110.50.35418550.8061100
2.51-2.610.60.30118280.8551100
2.6-2.6910.50.26918470.9051100
2.69-2.810.60.226184111100
2.8-2.9210.40.17918391.1011100
2.92-3.0810.40.14418661.2421100
3.08-3.2710.40.12118551.3881100
3.27-3.5210.30.09518721.7561100
3.52-3.8810.20.08418772.2811100
3.88-4.44100.0818873.091100
4.44-5.599.80.07819193.2691100
5.59-509.40.07620604.911100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.06→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2152 / WRfactor Rwork: 0.1719 / FOM work R set: 0.8246 / SU B: 4.505 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1641 / SU Rfree: 0.1612 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 1137 3.1 %RANDOM
Rwork0.1891 ---
obs0.1906 35715 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.9 Å2 / Biso mean: 35.898 Å2 / Biso min: 15.32 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å2-0 Å20 Å2
2---0.6 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.06→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 10 221 3606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193526
X-RAY DIFFRACTIONr_bond_other_d0.0010.023406
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9714816
X-RAY DIFFRACTIONr_angle_other_deg0.78337842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4875443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56923.973146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1515570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3081516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02803
X-RAY DIFFRACTIONr_mcbond_it1.9043.3951736
X-RAY DIFFRACTIONr_mcbond_other1.9023.3931735
X-RAY DIFFRACTIONr_mcangle_it2.6865.0782179
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 69 -
Rwork0.26 2583 -
all-2652 -
obs--98.26 %

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