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- PDB-5nyg: Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 - SG P2(1)... -

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Basic information

Entry
Database: PDB / ID: 5nyg
TitleAnbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 - SG P2(1)2(1)2(1)
ComponentsAnbu
KeywordsHYDROLASE / Ntn-hydrolase-fold / proteasome / evolution
Function / homologyUncharacterised conserved protein UCP009120, proteasome-type protease, Sll0069 / proteasome core complex / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / proteolysis involved in protein catabolic process / Peptidase
Function and homology information
Biological speciesHyphomicrobium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVielberg, M.-T. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: J. Mol. Biol. / Year: 2018
Title: On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral beta-Subunit Protein Anbu.
Authors: Vielberg, M.T. / Bauer, V.C. / Groll, M.
History
DepositionMay 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
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 / _pdbx_audit_support.funding_organization
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
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: Anbu
B: Anbu
C: Anbu
D: Anbu
E: Anbu
F: Anbu
G: Anbu
H: Anbu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,77712
Polymers220,2888
Non-polymers4894
Water13,619756
1
A: Anbu
E: Anbu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1943
Polymers55,0722
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-14 kcal/mol
Surface area20390 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23520 Å2
ΔGint-52 kcal/mol
Surface area74380 Å2
MethodPISA
3
B: Anbu
C: Anbu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1943
Polymers55,0722
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-19 kcal/mol
Surface area19960 Å2
MethodPISA
4
D: Anbu
F: Anbu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1943
Polymers55,0722
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-17 kcal/mol
Surface area20160 Å2
MethodPISA
5
H: Anbu
hetero molecules

G: Anbu


Theoretical massNumber of molelcules
Total (without water)55,1943
Polymers55,0722
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-x-1,y-1/2,-z-1/21
Buried area4480 Å2
ΔGint-20 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.250, 116.300, 197.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Anbu


Mass: 27536.016 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomicrobium sp. (strain MC1) (bacteria)
Gene: HYPMC_4374 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8JB59
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Di-sodium tatrate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 92239 / % possible obs: 98.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NYF

5nyf


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 17.986 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R Free: 0.25 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24202 4603 5 %RANDOM
Rwork0.20426 ---
obs0.20614 87461 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.954 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0 Å2-0 Å2
2--1.66 Å2-0 Å2
3----1.29 Å2
Refinement stepCycle: 1 / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14678 0 32 756 15466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01914970
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213942
X-RAY DIFFRACTIONr_angle_refined_deg0.991.9520207
X-RAY DIFFRACTIONr_angle_other_deg0.813332051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31151820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75323.115777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.982152515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.14115160
X-RAY DIFFRACTIONr_chiral_restr0.0560.22229
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023391
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.783.6757353
X-RAY DIFFRACTIONr_mcbond_other0.783.6737348
X-RAY DIFFRACTIONr_mcangle_it0.9445.4929146
X-RAY DIFFRACTIONr_mcangle_other0.9445.4939147
X-RAY DIFFRACTIONr_scbond_it0.6683.9177617
X-RAY DIFFRACTIONr_scbond_other0.6683.9177617
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8555.80711062
X-RAY DIFFRACTIONr_long_range_B_refined2.18542.92816078
X-RAY DIFFRACTIONr_long_range_B_other1.75642.68815931
X-RAY DIFFRACTIONr_rigid_bond_restr0.823328912
X-RAY DIFFRACTIONr_sphericity_free29.9655476
X-RAY DIFFRACTIONr_sphericity_bonded3.958528932
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 335 -
Rwork0.271 6374 -
obs--99.81 %
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)
10.43440.0835-0.07050.9019-0.07090.50180.0501-0.0083-0.0149-0.02320.0105-0.0755-0.02490.0358-0.06060.00780.00110.00310.08260.00070.0877-16.0126-1.854-32.3728
20.75610.21350.23091.32810.35290.72150.0241-0.1133-0.07780.0787-0.03230.08830.0606-0.04450.00820.07060.00710.06040.07980.03750.0716-61.3072-14.0243-11.0597
30.57780.2009-0.17270.8529-0.0360.62220.0065-0.14080.07420.0802-0.0133-0.0489-0.01620.07790.00680.02260.0042-0.02340.1096-0.02550.036-38.809212.268-11.9994
41.00090.30740.16310.4572-0.0850.5029-0.0529-0.12550.08610.0280.0247-0.0026-0.0622-0.07080.02830.05420.03670.01790.0841-0.02870.0395-69.281726.7276-13.5721
50.94510.25640.16770.9473-0.27160.6141-0.0176-0.0597-0.12360.18540.0004-0.03790.05880.01340.01720.09370.03670.01490.06030.03520.0414-31.6712-28.7569-15.237
60.4809-0.1850.26210.72210.41820.96620.0558-0.0805-0.0478-0.0247-0.01420.04550.1384-0.1301-0.04160.0458-0.03430.00790.0880.02060.0897-85.84010.4489-28.9634
70.7936-0.0868-0.26590.62740.18320.7415-0.07350.0831-0.0391-0.02760.02650.07830.0727-0.09990.0470.0318-0.0522-0.0040.0917-0.00180.0833-90.323915.1099-59.1388
80.6273-0.23770.25610.6051-0.09840.8904-0.05810.06060.0467-0.03050.0442-0.0496-0.08840.13340.01390.0328-0.04150.02930.0808-0.01150.0811-13.7884-16.7989-62.4848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 243
2X-RAY DIFFRACTION2B0 - 243
3X-RAY DIFFRACTION3C0 - 243
4X-RAY DIFFRACTION4D0 - 243
5X-RAY DIFFRACTION5E0 - 240
6X-RAY DIFFRACTION6F0 - 243
7X-RAY DIFFRACTION7G0 - 243
8X-RAY DIFFRACTION8H0 - 243

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