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- PDB-3r6m: Crystal structure of Vibrio parahaemolyticus YeaZ -

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Basic information

Entry
Database: PDB / ID: 3r6m
TitleCrystal structure of Vibrio parahaemolyticus YeaZ
ComponentsYeaZ, resuscitation promoting factor
KeywordsHYDROLASE / Actin/Hsp70 nucleotide-binding fold / bacterial resuscitation / viable but non-culturable state / resuscitation promoting factor / YgjD / YjeE / Vibrio parahaemolyticus
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine modification / cytosol
Similarity search - Function
tRNA threonylcarbamoyl adenosine modification protein TsaB / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRoujeinikova, A. / Aydin, I.
CitationJournal: Plos One / Year: 2011
Title: Structural Analysis of the Essential Resuscitation Promoting Factor YeaZ Suggests a Mechanism of Nucleotide Regulation through Dimer Reorganization.
Authors: Aydin, I. / Saijo-Hamano, Y. / Namba, K. / Thomas, C. / Roujeinikova, A.
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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 / 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: YeaZ, resuscitation promoting factor
B: YeaZ, resuscitation promoting factor
C: YeaZ, resuscitation promoting factor
D: YeaZ, resuscitation promoting factor


Theoretical massNumber of molelcules
Total (without water)91,2424
Polymers91,2424
Non-polymers00
Water00
1
A: YeaZ, resuscitation promoting factor
D: YeaZ, resuscitation promoting factor


Theoretical massNumber of molelcules
Total (without water)45,6212
Polymers45,6212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-18 kcal/mol
Surface area18750 Å2
MethodPISA
2
B: YeaZ, resuscitation promoting factor
C: YeaZ, resuscitation promoting factor


Theoretical massNumber of molelcules
Total (without water)45,6212
Polymers45,6212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-18 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.733, 63.844, 82.271
Angle α, β, γ (deg.)90.000, 104.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 2 - 213 / Label seq-ID: 2 - 213

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
YeaZ, resuscitation promoting factor


Mass: 22810.561 Da / Num. of mol.: 4 / Fragment: Residues 2-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: NCTC 10884 / Gene: VP0866, YeaZ / Plasmid: pET21bRPF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q87RD1

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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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 200 mM lithium acetate dihydrate, 30 mM Tris HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→79.489 Å / Num. all: 13608 / Num. obs: 13608 / % possible obs: 92.2 % / Redundancy: 2.5 % / Rsym value: 0.066 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.272.40.2932.6469819620.29390.9
3.27-3.472.50.1724.4475919310.17294.5
3.47-3.712.50.1275.5451718210.12794.3
3.71-42.50.0946.8411416620.09493.8
4-4.382.50.078.7373315060.0793.1
4.38-4.92.50.0579.8348413810.05792.5
4.9-5.662.50.05410.5300911970.05492
5.66-6.932.50.0511.5255710190.0591.1
6.93-9.82.50.04712.118877500.04789.2
9.8-49.7772.30.0578.88903790.05778.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GEL

2gel


Resolution: 3.1→79.489 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.871 / Occupancy max: 1 / Occupancy min: 1 / SU B: 64.537 / SU ML: 0.532 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.664 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2939 687 5.1 %RANDOM 5%
Rwork0.2387 ---
obs0.2415 13599 89.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 228.56 Å2 / Biso mean: 96.4599 Å2 / Biso min: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å2-0.61 Å2
2--0.75 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 3.1→79.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6162 0 0 0 6162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226266
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9598567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3335844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.8624.857245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.12715919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1141533
X-RAY DIFFRACTIONr_chiral_restr0.110.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214757
X-RAY DIFFRACTIONr_mcbond_it0.5231.54200
X-RAY DIFFRACTIONr_mcangle_it0.96326661
X-RAY DIFFRACTIONr_scbond_it1.13432066
X-RAY DIFFRACTIONr_scangle_it1.9534.51906
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A848TIGHT POSITIONAL0.040.05
2B848TIGHT POSITIONAL0.050.05
3C848TIGHT POSITIONAL0.050.05
4D848TIGHT POSITIONAL0.050.05
1A691MEDIUM POSITIONAL0.050.5
2B691MEDIUM POSITIONAL0.050.5
3C691MEDIUM POSITIONAL0.050.5
4D691MEDIUM POSITIONAL0.050.5
1A848TIGHT THERMAL0.070.5
2B848TIGHT THERMAL0.080.5
3C848TIGHT THERMAL0.070.5
4D848TIGHT THERMAL0.080.5
1A691MEDIUM THERMAL0.082
2B691MEDIUM THERMAL0.12
3C691MEDIUM THERMAL0.082
4D691MEDIUM THERMAL0.092
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 54 -
Rwork0.288 912 -
all-966 -
obs--86.95 %
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)
17.73452.6159-5.67156.1429-3.935812.30250.23540.1492-0.2769-0.3136-0.3361-0.23110.83780.45180.10060.3070.295-0.05840.4955-0.02890.476955.6097.56426.651
28.3111-2.77425.72366.1434-3.816611.41280.2522-0.340.43240.268-0.3231-0.2135-0.69190.21280.07080.2904-0.3013-0.04630.5253-0.06530.470555.71522.53152.72
313.18676.83083.98287.40224.31886.35930.5823-1.1573-1.78511.023-0.5446-0.73780.4837-0.2462-0.03770.5199-0.1371-0.12210.60910.3420.758943.158-7.92865.607
411.115.1518-2.92817.1824-3.18935.36590.3279-0.64311.3830.7424-0.34650.2724-0.42560.09650.01860.482-0.105-0.04660.5049-0.23940.671417.6996.03365.728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 213
2X-RAY DIFFRACTION2B2 - 213
3X-RAY DIFFRACTION3C2 - 213
4X-RAY DIFFRACTION4D2 - 213

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