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- PDB-4ohr: Crystal structure of MilB from Streptomyces rimofaciens -

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Basic information

Entry
Database: PDB / ID: 4ohr
TitleCrystal structure of MilB from Streptomyces rimofaciens
ComponentsCMP/hydroxymethyl CMP hydrolase
KeywordsHYDROLASE
Function / homologyNucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CMP/hydroxymethyl CMP hydrolase
Function and homology information
Biological speciesStreptomyces rimofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CMP/hydroxymethyl CMP hydrolase


Theoretical massNumber of molelcules
Total (without water)20,5281
Polymers20,5281
Non-polymers00
Water3,297183
1


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

A: CMP/hydroxymethyl CMP hydrolase


Theoretical massNumber of molelcules
Total (without water)41,0562
Polymers41,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2710 Å2
ΔGint-23 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.294, 102.000, 81.956
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CMP/hydroxymethyl CMP hydrolase


Mass: 20528.025 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.49 Å3/Da / Density % sol: 50.63 % / Mosaicity: 0.579 °
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: 1.8→50 Å / Num. obs: 17809 / % possible obs: 96.4 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.104 / Χ2: 1.004 / Net I/σ(I): 18.6
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.8614.40.2871815199.9
1.86-1.9480.40615841.00587.7
1.94-2.0313.20.23918111.00399.9
2.03-2.1311.30.19118321.005100
2.13-2.2711.70.14516601.00891
2.27-2.4413.60.12418371.00599.6
2.44-2.6913.40.11818451.00699.9
2.69-3.0813.90.1118451.00799.9
3.08-3.8810.30.08717070.99791
3.88-5012.60.0711873194.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.847 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 908 5.1 %RANDOM
Rwork0.1828 ---
obs0.1845 17659 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.85 Å2 / Biso mean: 25.926 Å2 / Biso min: 9.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2---1.19 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 0 183 1385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191228
X-RAY DIFFRACTIONr_bond_other_d0.0010.021160
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9511667
X-RAY DIFFRACTIONr_angle_other_deg0.75432657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1245157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.97622.80757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49715188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8191512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02290
X-RAY DIFFRACTIONr_mcbond_it0.7891.656631
X-RAY DIFFRACTIONr_mcbond_other0.7851.652630
X-RAY DIFFRACTIONr_mcangle_it1.3522.475787
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 70 -
Rwork0.184 1256 -
all-1326 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 20.0495 Å / Origin y: -12.0326 Å / Origin z: 3.766 Å
111213212223313233
T0.0221 Å2-0.0049 Å2-0.0148 Å2-0.0284 Å2-0.0007 Å2--0.0262 Å2
L0.8582 °2-0.2676 °2-0.1769 °2-1.7092 °2-0.5042 °2--1.7214 °2
S0.0766 Å °0.0225 Å °-0.0062 Å °-0.1456 Å °-0.011 Å °0.0726 Å °0.081 Å °-0.0231 Å °-0.0656 Å °

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