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- PDB-6hb3: Structure of Hgh1, crystal form II -

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Basic information

Entry
Database: PDB / ID: 6hb3
TitleStructure of Hgh1, crystal form II
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: 3 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 1.3May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)167,5664
Polymers167,5664
Non-polymers00
Water00
1
A: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)41,8911
Polymers41,8911
Non-polymers00
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)41,8911
Polymers41,8911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein HGH1


Theoretical massNumber of molelcules
Total (without water)41,8911
Polymers41,8911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)191.798, 69.643, 206.866
Angle α, β, γ (deg.)90.000, 93.750, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA0 - 3566 - 362
21GLUGLUBB0 - 3566 - 362
12GLYGLYAA0 - 3556 - 361
22GLYGLYCC0 - 3556 - 361
13PROPROAA0 - 3576 - 363
23PROPRODD0 - 3576 - 363
14GLYGLYBB-1 - 3555 - 361
24GLYGLYCC-1 - 3555 - 361
15GLUGLUBB0 - 3566 - 362
25GLUGLUDD0 - 3566 - 362
16GLYGLYCC0 - 3556 - 361
26GLYGLYDD0 - 3556 - 361

NCS ensembles :
ID
1
2
3
4
5
6

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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) / Variant (production host): Rosetta 2 (DE3) / References: UniProt: P48362

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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: 4.11 Å3/Da / Density % sol: 70.1 % / Mosaicity: 0.12 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 16% PEG-3350, 0.1 M Na3-citrate and 20 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3→47.96 Å / Num. obs: 54838 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.066 / Rrim(I) all: 0.123 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.093.50.7721470442460.7930.4820.9131.595
12.72-47.963.40.02426077750.9990.0150.02935.598

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation47.96 Å3.2 Å

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Processing

Software
NameVersionClassification
XDSVERSION January 10, 2014data reduction
Aimless0.1.27data scaling
MOLREP11.0.05phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 35.422 / SU ML: 0.273 / SU R Cruickshank DPI: 0.9234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.923 / ESU R Free: 0.331
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 2790 5.1 %RANDOM
Rwork0.2197 ---
obs0.2202 52045 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 171.82 Å2 / Biso mean: 73.132 Å2 / Biso min: 40.79 Å2
Baniso -1Baniso -2Baniso -3
1--3.36 Å20 Å2-0.21 Å2
2--3.55 Å20 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11485 0 0 0 11485
Num. residues----1434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01911684
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211566
X-RAY DIFFRACTIONr_angle_refined_deg0.9541.99215767
X-RAY DIFFRACTIONr_angle_other_deg0.811326715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75451430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62724.887532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.576152248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.681568
X-RAY DIFFRACTIONr_chiral_restr0.0570.21815
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112905
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022459
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A241790.05
12B241790.05
21A241360.05
22C241360.05
31A242050.05
32D242050.05
41B243760.03
42C243760.03
51B240540.06
52D240540.06
61C240110.06
62D240110.06
LS refinement shellResolution: 3→3.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 178 -
Rwork0.37 3644 -
all-3822 -
obs--96.15 %
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)
11.85940.6088-1.19551.8664-0.77474.39760.0006-0.05680.04340.26340.01080.12250.3175-0.2058-0.01140.2290.02040.01390.0378-0.04660.221448.2584.42416.175
25.49440.6678-0.56860.6761-0.22631.0144-0.18360.9947-0.2122-0.08040.0065-0.0408-0.0654-0.04630.17710.348-0.01660.04950.4381-0.10250.219198.9637.816-27.619
36.0991-0.734-0.55460.63890.34560.7417-0.154-1.2294-0.2810.0825-0.05560.0532-0.04140.05720.20950.32780.03250.0650.51450.16510.2081-9.7793.534130.857
41.9465-0.6008-1.48351.79760.77424.1839-0.04370.0507-0.1064-0.25550.0907-0.03990.26830.1068-0.0470.218-0.05610.00540.03410.01420.206240.5760.16886.921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 357
2X-RAY DIFFRACTION2B-1 - 358
3X-RAY DIFFRACTION3C-1 - 356
4X-RAY DIFFRACTION4D0 - 357

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