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- PDB-6hb1: Structure of Hgh1, crystal form I -

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Basic information

Entry
Database: PDB / ID: 6hb1
TitleStructure of Hgh1, crystal form I
ComponentsProtein HGH1
KeywordsCHAPERONE / solenoid protein / Armadillo repeat
Function / homology
Function and homology information


translation elongation factor binding / : / nucleus / cytoplasm
Similarity search - Function
Protein HGH1 N-terminal / Protein HGH1 C-terminal / Protein Hgh1 / Domain of unknown function (DUF383) / Domain of unknown function (DUF384) / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsMoenkemeyer, L. / Klaips, C.L. / Balchin, D. / Koerner, R. / Hartl, F.U. / Bracher, A.
CitationJournal: Mol.Cell / Year: 2019
Title: Chaperone Function of Hgh1 in the Biogenesis of Eukaryotic Elongation Factor 2.
Authors: Monkemeyer, L. / Klaips, C.L. / Balchin, D. / Korner, R. / Hartl, F.U. / Bracher, A.
History
DepositionAug 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 17, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein HGH1
B: Protein HGH1
C: Protein HGH1
D: Protein HGH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,6727
Polymers167,5664
Non-polymers1063
Water7,260403
1
A: Protein HGH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9272
Polymers41,8911
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)41,8911
Polymers41,8911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein HGH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9272
Polymers41,8911
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein HGH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9272
Polymers41,8911
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.207, 86.427, 88.368
Angle α, β, γ (deg.)118.480, 105.800, 99.150
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein HGH1 / HMG1/2 protein homolog


Mass: 41891.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: HGH1, YGR187C, G7538 / Plasmid: pProEX-HtB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P48362
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.91 Å3/Da / Density % sol: 57.67 % / Mosaicity: 0.12 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG-3350, 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.5 and 20 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.33→44.2 Å / Num. obs: 79967 / % possible obs: 98.8 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.044 / Rrim(I) all: 0.116 / Net I/σ(I): 11.5 / Num. measured all: 552895 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.33-2.374.80.91142190.5970.441.01791.2
11.87-44.27.40.0736040.9960.0290.07998.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSVERSION January 10, 2014data reduction
Aimless0.1.27data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HB2

6hb2


Resolution: 2.33→29.303 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.13 / Phase error: 25.64
RfactorNum. reflection% reflection
Rfree0.2262 7999 5.03 %
Rwork0.1766 --
obs0.179 159137 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 182.95 Å2 / Biso mean: 63.3313 Å2 / Biso min: 25.11 Å2
Refinement stepCycle: final / Resolution: 2.33→29.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11430 0 3 403 11836
Biso mean--126.62 50.37 -
Num. residues----1429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311657
X-RAY DIFFRACTIONf_angle_d0.68315736
X-RAY DIFFRACTIONf_chiral_restr0.0291812
X-RAY DIFFRACTIONf_plane_restr0.0032018
X-RAY DIFFRACTIONf_dihedral_angle_d12.7314486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.33-2.35650.42622620.33634706496891
2.3565-2.38420.32682790.29844961524099
2.3842-2.41320.32312480.28215038528699
2.4132-2.44380.33152440.27124995523999
2.4438-2.47590.35932320.26725024525696
2.4759-2.50980.2842980.25175011530999
2.5098-2.54560.27752410.24585092533399
2.5456-2.58360.29542900.23195027531799
2.5836-2.6240.2842560.24175046530299
2.624-2.6670.31332640.23545047531199
2.667-2.71290.29453150.22634990530599
2.7129-2.76220.24422410.21755154539599
2.7622-2.81530.2872890.22314975526499
2.8153-2.87270.27052810.22745105538699
2.8727-2.93510.36672580.23055048530699
2.9351-3.00330.31692800.21495031531199
3.0033-3.07840.25342640.20145020528498
3.0784-3.16150.24192740.19815006528099
3.1615-3.25440.24322400.202751205360100
3.2544-3.35930.26342560.20115072532899
3.3593-3.47920.24082860.19385031531799
3.4792-3.61830.22652580.17265113537199
3.6183-3.78260.18162760.153150275303100
3.7826-3.98160.19772860.14775031531798
3.9816-4.23040.18092640.140251415405100
4.2304-4.55590.18062760.129650395315100
4.5559-5.01230.17352420.123751215363100
5.0123-5.73290.17092710.140550955366100
5.7329-7.2050.2072590.15585052531199
7.205-29.30520.1652690.13075020528999
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)
11.62580.84141.15151.44830.61442.0456-0.1074-0.05640.0894-0.08190.00930.1549-0.1034-0.28340.0770.32470.05860.06880.35890.0170.3091-57.1774-12.1323-33.2669
22.9172-0.4971.96221.0387-0.56432.114-0.16180.30050.45360.0361-0.0237-0.1276-0.02930.30230.16110.38880.0410.06290.39180.03580.3716-0.4807-0.1686-0.3793
33.30151.12430.09181.19710.22940.7283-0.0977-0.2888-0.3050.0371-0.0094-0.1042-0.08460.07060.0760.4320.04620.01960.36860.11470.338629.4979-31.732613.8934
43.3542-0.66840.61111.007-0.34270.89590.19850.4104-0.5742-0.10810.00050.03430.20330.1406-0.20720.45120.02520.02650.3365-0.11540.4645-29.7773-44.4112-14.3253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 358 )A2 - 358
2X-RAY DIFFRACTION2chain 'B' and (resid 0 through 356 )B0 - 356
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 356 )C1 - 356
4X-RAY DIFFRACTION4chain 'D' and (resid -1 through 357 )D-1 - 357

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