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- PDB-5jnh: Crystal Structure of cytidine monophosphate hydroxymethylase MilA -

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Basic information

Entry
Database: PDB / ID: 5jnh
TitleCrystal Structure of cytidine monophosphate hydroxymethylase MilA
ComponentsCMP 5-hydroxymethylase
KeywordsTRANSFERASE / CMP hydroxymethylase
Function / homologyThymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / methyltransferase activity / methylation / CMP 5-hydroxymethylase
Function and homology information
Biological speciesStreptomyces rimofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.202 Å
AuthorsZhao, G. / He, X.
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis of the substrate preference towards CMP for a thymidylate synthase MilA involved in mildiomycin biosynthesis
Authors: Zhao, G. / Chen, C. / Xiong, W. / Gao, T. / Deng, Z. / Wu, G. / He, X.
History
DepositionApr 30, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: CMP 5-hydroxymethylase
B: CMP 5-hydroxymethylase


Theoretical massNumber of molelcules
Total (without water)76,9962
Polymers76,9962
Non-polymers00
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-15 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.752, 107.752, 112.024
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-570-

HOH

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Components

#1: Protein CMP 5-hydroxymethylase / cytidine monophosphate hydroxymethylase MilA


Mass: 38498.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rimofaciens (bacteria) / Gene: milA / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4Y380
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5
Details: 15% (w/v) polyethylene glycol 3350, 0.08 M Lithium sulfate monohydrate, 0.1 M Tris HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03576 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03576 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 38532 / % possible obs: 100 % / Redundancy: 21.8 % / Biso Wilson estimate: 26.43 Å2 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.034 / Rrim(I) all: 0.16 / Χ2: 1.002 / Net I/av σ(I): 23.235 / Net I/σ(I): 7 / Num. measured all: 838384
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.28190.7671100
2.28-2.3721.60.6361100
2.37-2.4822.30.521100
2.48-2.6122.40.3941100
2.61-2.7722.40.3011100
2.77-2.9922.30.2181100
2.99-3.2922.30.1451100
3.29-3.7622.20.1011100
3.76-4.74220.1031100
4.74-5021.10.0721100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.202→48.025 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.43
RfactorNum. reflection% reflection
Rfree0.207 1875 4.87 %
Rwork0.1679 --
obs0.1698 38497 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.82 Å2 / Biso mean: 27.3189 Å2 / Biso min: 11.42 Å2
Refinement stepCycle: final / Resolution: 2.202→48.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 0 336 5410
Biso mean---32.63 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085216
X-RAY DIFFRACTIONf_angle_d0.8067095
X-RAY DIFFRACTIONf_chiral_restr0.047744
X-RAY DIFFRACTIONf_plane_restr0.005939
X-RAY DIFFRACTIONf_dihedral_angle_d14.4943037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2024-2.26190.23091670.177227582925
2.2619-2.32850.2391430.173227622905
2.3285-2.40360.24921420.175627902932
2.4036-2.48950.2451430.183228042947
2.4895-2.58920.21531550.176727822937
2.5892-2.7070.24711470.17127782925
2.707-2.84970.22531390.180427872926
2.8497-3.02830.2441070.178928492956
3.0283-3.2620.24551510.170328082959
3.262-3.59020.19481550.165928212976
3.5902-4.10950.1811320.150628372969
4.1095-5.17650.1631570.14228663023
5.1765-48.03620.18521370.186329803117

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