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- PDB-4ohb: Crystal structure of MilB E103A in complex with 5-hydroxymethylcy... -

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Basic information

Entry
Database: PDB / ID: 4ohb
TitleCrystal structure of MilB E103A in complex with 5-hydroxymethylcytidine 5'-monophosphate (hmCMP) from Streptomyces rimofaciens
ComponentsCMP/hydroxymethyl CMP hydrolase
KeywordsHYDROLASE / protein-hmCMP complex
Function / homologyNucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-5HM / CMP/hydroxymethyl CMP hydrolase
Function and homology information
Biological speciesStreptomyces rimofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsZhao, G. / Zhang, Y. / Liu, G. / Wu, G. / He, X.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structure of the N-glycosidase MilB in complex with hydroxymethyl CMP reveals its Arg23 specifically recognizes the substrate and controls its entry
Authors: Zhao, G. / Wu, G. / Zhang, Y. / Liu, G. / Han, T. / Deng, Z. / He, X.
History
DepositionJan 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references / Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CMP/hydroxymethyl CMP hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8232
Polymers20,4701
Non-polymers3531
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CMP/hydroxymethyl CMP hydrolase
hetero molecules

A: CMP/hydroxymethyl CMP hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6464
Polymers40,9402
Non-polymers7062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2690 Å2
ΔGint-27 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.426, 101.808, 81.744
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

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Components

#1: Protein CMP/hydroxymethyl CMP hydrolase


Mass: 20469.988 Da / Num. of mol.: 1 / Mutation: E103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rimofaciens (bacteria) / Gene: MilB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4Y381
#2: Chemical ChemComp-5HM / 5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) / 5-hydroxymethylcytidine 5'-monophosphate


Type: RNA linking / Mass: 353.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N3O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.31 Å3/Da / Density % sol: 46.72 % / Mosaicity: 0.827 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG 4000, 0.08M Magnesium chloride hexahydrate, 0.1M Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 13.3 % / Number: 122549 / Rmerge(I) obs: 0.143 / Χ2: 1 / D res high: 2.25 Å / D res low: 50 Å / Num. obs: 9244 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.855099.710.0840.99913.3
3.854.8594.510.0960.99812.9
3.363.8596.810.160.99511.5
3.053.3610010.1120.99714.4
2.833.0510010.1410.99214.5
2.672.8310010.2010.99314.5
2.532.6710010.3131.00714.3
2.422.5310010.2861.00714
2.332.4299.810.3370.99212.7
2.252.3393.610.5031.00510.4
ReflectionResolution: 2.4→50 Å / Num. obs: 7108 / % possible obs: 92.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.125 / Χ2: 1 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.494.20.467351.00698.7
2.49-2.594.50.3747361.00497.9
2.59-2.73.70.4417040.99492.8
2.7-2.854.60.2517520.99397.9
2.85-3.024.70.1827511.00598.3
3.02-3.264.70.1447451.00397.8
3.26-3.584.20.1236340.99783.9
3.58-4.13.90.1164940.99963.2
4.1-5.174.70.0917640.99796.6
5.17-504.40.0697930.99894.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.4→43.25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.351 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.257 330 4.7 %RANDOM
Rwork0.1924 ---
obs0.1954 7060 91.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.87 Å2 / Biso mean: 41.159 Å2 / Biso min: 21.33 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å20 Å2
2---2.04 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1206 0 23 37 1266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191268
X-RAY DIFFRACTIONr_bond_other_d0.0010.021187
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9731725
X-RAY DIFFRACTIONr_angle_other_deg0.85432720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54622.58658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19415191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0941513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02302
X-RAY DIFFRACTIONr_mcbond_it3.2743.901640
X-RAY DIFFRACTIONr_mcbond_other3.2743.896639
X-RAY DIFFRACTIONr_mcangle_it5.0465.832800
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 16 -
Rwork0.261 503 -
all-519 -
obs--95.4 %

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