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- PDB-8ztq: Crystal structure of Sufu from Mycoplasma Pneumonia -

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Basic information

Entry
Database: PDB / ID: 8ztq
TitleCrystal structure of Sufu from Mycoplasma Pneumonia
ComponentsNitrogen fixation protein NifU
KeywordsBIOSYNTHETIC PROTEIN / Sufs / Mycoplasma Pneumonia / PLP-binding / L-Cys
Function / homologyNIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / iron-sulfur cluster assembly / iron-sulfur cluster binding / iron ion binding / Nitrogen fixation protein NifU
Function and homology information
Biological speciesMycoplasmoides pneumoniae 19294 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.889 Å
AuthorsWang, W.M. / Ma, D.Y. / Gong, W.J. / Yao, H. / Liu, Y.H. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: The reduced interaction between SufS and SufU in Mycoplasma penetrans results in diminished sulfotransferase activity.
Authors: Ma, D. / Yao, H. / Liu, Y. / Gong, W. / Zhao, Y. / Wang, R. / Wu, C. / Wang, W. / Wang, H.
History
DepositionJun 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogen fixation protein NifU
B: Nitrogen fixation protein NifU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9294
Polymers35,7992
Non-polymers1312
Water70339
1
A: Nitrogen fixation protein NifU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9652
Polymers17,8991
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nitrogen fixation protein NifU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9652
Polymers17,8991
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.080, 30.333, 87.209
Angle α, β, γ (deg.)90.00, 122.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nitrogen fixation protein NifU / MpeSufu


Mass: 17899.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Mycoplasmoides pneumoniae 19294 is not available, replaced by Q8EV25 temporarily.
Source: (gene. exp.) Mycoplasmoides pneumoniae 19294 (bacteria)
Gene: MYPE7420 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EV25
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: BIS-TRIS, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.889→50 Å / Num. obs: 7613 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.088 / Rrim(I) all: 0.217 / Χ2: 1.028 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.9-2.954.60.783780.7120.9120.3870.8750.62498.7
2.95-34.70.6063770.8060.9450.3010.6790.66999.2
3-3.065.10.6243610.8490.9580.2990.6950.66799.4
3.06-3.125.60.6693710.830.9530.3090.740.67899.5
3.12-3.195.80.5563660.8870.970.2490.610.696100
3.19-3.275.70.5223700.8690.9640.2390.5760.661100
3.27-3.356.20.4244020.920.9790.1850.4640.736100
3.35-3.446.40.4293570.9590.9890.1830.4680.776100
3.44-3.546.40.3753710.920.9790.160.4080.824100
3.54-3.656.50.2943980.9520.9880.1230.3190.95100
3.65-3.786.30.2423960.9650.9910.1040.2631.077100
3.78-3.945.90.2163510.9630.990.0960.2371.114100
3.94-4.116.30.1913750.9790.9950.0810.2081.174100
4.11-4.336.20.1773880.9810.9950.0760.1931.253100
4.33-4.66.30.1563690.9820.9950.0670.171.454100
4.6-4.966.40.1413970.9820.9960.060.1541.46899.7
4.96-5.466.10.1473810.9820.9950.0640.1611.206100
5.46-6.2460.1453930.9790.9950.0650.161.136100
6.24-7.8660.1153870.9860.9970.050.1261.103100
7.86-505.30.0994250.9880.9970.0480.111.91399.5

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.889→36.783 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2992 759 9.99 %
Rwork0.2711 --
obs0.2739 7598 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.889→36.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 2 41 2375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032359
X-RAY DIFFRACTIONf_angle_d0.5653173
X-RAY DIFFRACTIONf_dihedral_angle_d15.751457
X-RAY DIFFRACTIONf_chiral_restr0.042368
X-RAY DIFFRACTIONf_plane_restr0.003408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.889-3.11150.39741390.34421254X-RAY DIFFRACTION91
3.1115-3.42440.39861530.30251370X-RAY DIFFRACTION100
3.4244-3.91950.29991610.27281366X-RAY DIFFRACTION100
3.9195-4.93620.27661490.23131386X-RAY DIFFRACTION100
4.9362-36.7830.25121570.27111463X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.4092 Å / Origin y: -4.3195 Å / Origin z: 18.3537 Å
111213212223313233
T0.3781 Å20.0194 Å20.0111 Å2-0.3873 Å20.0105 Å2--0.3511 Å2
L1.4235 °20.5326 °21.2133 °2-0.0884 °20.3207 °2--0.5291 °2
S0.1114 Å °-0.0517 Å °0.2109 Å °-0.0059 Å °-0.0431 Å °-0.0453 Å °0.2247 Å °-0.1489 Å °-0.1268 Å °
Refinement TLS groupSelection details: all

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