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- PDB-3u12: The pleckstrin homology (PH) domain of USP37 -

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Basic information

Entry
Database: PDB / ID: 3u12
TitleThe pleckstrin homology (PH) domain of USP37
ComponentsUSP37 protein
KeywordsHYDROLASE / Structural Genomics / PH-domain / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cysteine-type deubiquitinase activity => GO:0004843 / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein deubiquitination / regulation of DNA replication / G1/S transition of mitotic cell cycle / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases ...cysteine-type deubiquitinase activity => GO:0004843 / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein deubiquitination / regulation of DNA replication / G1/S transition of mitotic cell cycle / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cell division / cysteine-type endopeptidase activity / protein kinase binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 26/29/37, pleckstrin homology-like domain / Ubiquitin carboxyl-terminal hydrolase 37, pleckstrin homology-like domain / Ubiquitin carboxyl-terminal hydrolase 37, pleckstrin homology-like domain superfamily / N-terminal of ubiquitin carboxyl-terminal hydrolase 37 / Ubiquitin interaction motif / Ubiquitin-interacting motif. / 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 26/29/37, pleckstrin homology-like domain / Ubiquitin carboxyl-terminal hydrolase 37, pleckstrin homology-like domain / Ubiquitin carboxyl-terminal hydrolase 37, pleckstrin homology-like domain superfamily / N-terminal of ubiquitin carboxyl-terminal hydrolase 37 / Ubiquitin interaction motif / Ubiquitin-interacting motif. / 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. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / PH-domain like / Papain-like cysteine peptidase superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Ubiquitin carboxyl-terminal hydrolase 37 / Ubiquitinyl hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsDong, A. / Nair, U.B. / Wernimont, A. / Walker, J.R. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The pleckstrin homology (PH) domain of USP37
Authors: Dong, A. / Nair, U.B. / Wernimont, A. / Walker, J.R. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: USP37 protein
B: USP37 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,30739
Polymers31,6812
Non-polymers62637
Water1,53185
1
A: USP37 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,18826
Polymers15,8401
Non-polymers34725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: USP37 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,12013
Polymers15,8401
Non-polymers27912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.083, 64.083, 218.814
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-132-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein USP37 protein / Uncharacterized protein


Mass: 15840.454 Da / Num. of mol.: 2 / Fragment: residues 4-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP37 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q86W68, UniProt: Q86T82*PLUS

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Non-polymers , 5 types, 122 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 29 / Source method: obtained synthetically
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Sodium acetate pH 5.6, 2.46 M ammonium sulfate, 10 mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 22, 2011
Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. all: 17041 / Num. obs: 17041 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.3 % / Biso Wilson estimate: 26.08 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 52.14
Reflection shellResolution: 2.08→2.12 Å / Redundancy: 19.7 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 4.6 / Num. unique all: 823 / Rsym value: 0.794 / % possible all: 100

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Processing

Software
NameVersionClassification
CMCFdata collection
PHASERphasing
SOLVEphasing
RESOLVEmodel building
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→19.74 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.9246 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 848 5.06 %RANDOM
Rwork0.2092 ---
all0.2103 16841 --
obs0.2103 16750 --
Displacement parametersBiso mean: 34.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.4143 Å20 Å20 Å2
2---0.4143 Å20 Å2
3---0.8285 Å2
Refine analyzeLuzzati coordinate error obs: 0.328 Å
Refinement stepCycle: LAST / Resolution: 2.08→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 65 85 1739
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011702HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.032303HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d599SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes248HARMONIC5
X-RAY DIFFRACTIONt_it1702HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion17.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion226SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1906SEMIHARMONIC4
LS refinement shellResolution: 2.08→2.22 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2181 158 5.53 %
Rwork0.1975 2699 -
all0.1987 2857 -
obs-2857 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2257-0.60030.76925.3561-0.93314.5420.0739-0.10.03020.1456-0.1586-0.34350.00290.46170.0847-0.11190.0428-0.0374-0.04920.1325-0.043-1.89114.403413.4215
24.0989-0.7892-0.41391.8753-1.04124.52820.08240.3344-0.1027-0.2435-0.00250.28740.2574-0.2808-0.0799-0.08360.0076-0.0849-0.06650.09240.0036-25.218918.20614.7372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 106
2X-RAY DIFFRACTION2{ B|* }B2 - 107

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