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- PDB-5b6d: Crystal Structure of cytidine monophosphate hydroxymethylase MilA... -

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Basic information

Entry
Database: PDB / ID: 5b6d
TitleCrystal Structure of cytidine monophosphate hydroxymethylase MilA with CMP
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 / CYTIDINE-5'-MONOPHOSPHATE / CMP 5-hydroxymethylase
Function and homology information
Biological speciesStreptomyces rimofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGong, Z. / Wu, 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
DepositionMay 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7024
Polymers73,0562
Non-polymers6462
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-32 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.601, 109.601, 113.432
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
11A-771-

HOH

21B-731-

HOH

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Components

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


Mass: 36528.031 Da / Num. of mol.: 2 / Fragment: UNP residues 5-329
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: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5
Details: 0.1 M sodium cacodylate trihydrate(pH 6.5), 1.4 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97912 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: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 91579 / % possible obs: 96.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.86 Å2 / Rmerge(I) obs: 0.132 / Net I/av σ(I): 13.553 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.65-1.716.90.8851100
1.71-1.786.70.6491100
1.78-1.866.70.4591100
1.86-1.9660.351194.2
1.96-2.086.90.2381100
2.08-2.246.50.192193.9
2.24-2.466.90.154185.5
2.46-2.826.70.1341100
2.82-3.5570.1141100
3.55-506.30.094192.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JNH
Resolution: 1.65→47.459 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.61
RfactorNum. reflection% reflection
Rfree0.1935 4588 5.01 %
Rwork0.1714 --
obs0.1726 91516 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.17 Å2 / Biso mean: 24.5545 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: final / Resolution: 1.65→47.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5061 0 42 547 5650
Biso mean--18.61 35.37 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065254
X-RAY DIFFRACTIONf_angle_d0.8117157
X-RAY DIFFRACTIONf_chiral_restr0.051753
X-RAY DIFFRACTIONf_plane_restr0.006941
X-RAY DIFFRACTIONf_dihedral_angle_d14.4533044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.66880.30711680.264429323100100
1.6688-1.68840.29451600.245829913151100
1.6884-1.7090.2731600.236529643124100
1.709-1.73060.28081400.222529683108100
1.7306-1.75340.2631510.213829923143100
1.7534-1.77740.23321340.197629963130100
1.7774-1.80280.24661500.195629963146100
1.8028-1.82970.19981450.177430053150100
1.8297-1.85830.22091690.181129693138100
1.8583-1.88880.2481640.17929683132100
1.8888-1.92140.43241240.372553267785
1.9214-1.95630.21961620.2152883304597
1.9563-1.99390.19161350.170929873122100
1.9939-2.03460.19591330.15730083141100
2.0346-2.07890.19451680.160829653133100
2.0789-2.12720.17191620.160330003162100
2.1272-2.18040.1931550.162829873142100
2.1804-2.23940.18261590.15952402256182
2.2394-2.30530.2001930.16641683177657
2.3053-2.37970.2041640.160530053169100
2.3797-2.46470.17921630.157630003163100
2.4647-2.56340.19271610.161329753136100
2.5634-2.68010.18741880.161229853173100
2.6801-2.82130.17631540.174130183172100
2.8213-2.99810.21541770.171429963173100
2.9981-3.22950.18851600.169830463206100
3.2295-3.55440.16491610.161330213182100
3.5544-4.06850.1681290.1522326245576
4.0685-5.12490.14931550.135630953250100
5.1249-47.47820.17621440.175232123356100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5696-0.35740.15660.62150.0080.62830.04250.0995-0.0505-0.0741-0.03290.0414-0.0179-0.017400.159-0.0117-0.00640.1441-0.00770.1243-17.2962.3161118.7462
20.1639-0.0359-0.14150.2674-0.02980.3103-0.0963-0.12640.01360.10750.130.1447-0.0365-0.026-00.19010.01170.00480.14920.0050.1899-22.918370.2184137.5918
30.2278-0.0420.17370.29830.30210.48080.0979-0.18910.01830.0331-0.0036-0.0402-0.00530.078100.1727-0.0176-0.00630.1644-0.0130.1504-1.804968.0399138.0375
40.0586-0.0510.11630.66540.00060.22870.0399-0.02140.03060.00630.00580.0686-0.02320.022400.1404-0.01950.00610.1530.00350.1172-7.071860.2107130.9214
50.3336-0.32580.1790.255-0.05920.23950.0195-0.0029-0.0223-0.1206-0.03240.0535-0.0438-0.0335-00.1506-0.0152-0.00870.1206-0.00280.1205-13.559665.1503121.1058
60.3834-0.5412-0.07680.72730.07140.364-0.03530.02940.14570.00980.0157-0.0602-0.08080.005700.2338-0.0158-0.01020.10770.01750.1936-15.303886.2603127.7321
70.10590.1970.08930.4366-0.16570.39610.10350.12620.2503-0.2324-0.02520.2044-0.2521-0.2025-0.00010.27210.0287-0.02930.1840.0210.239-25.510884.5286117.8654
80.2526-0.2837-0.19720.8542-0.4310.4704-0.00050.0037-0.0789-0.1392-0.0205-0.07610.08990.0982-00.1947-0.00480.00610.1642-0.01720.12476.45143.3285123.1022
90.1282-0.1877-0.15530.8480.03420.3486-0.1262-0.1350.02990.18480.134-0.04980.02480.063900.19730.02810.00170.17610.020.15581.697644.9507143.358
100.3538-0.6116-0.07990.9249-0.0350.26420.009-0.1785-0.09630.08430.0234-0.01290.03120.0167-00.1614-0.0125-0.00440.17390.0020.1443-4.834352.2595135.966
110.4173-0.3162-0.05380.72390.01450.26270.0031-0.025-0.037-0.1749-0.01170.02390.08880.0880.00010.17690.0104-0.00080.1416-0.00190.13011.704742.6447126.4927
120.9987-0.3180.12411.004-0.07460.3798-0.0823-0.2735-0.44750.07090.12540.16250.0723-0.079600.22840.0270.04910.18830.07480.28832.296325.1845141.997
130.2483-0.0914-0.0630.4924-0.09890.3015-0.0613-0.0168-0.2502-0.01150.0514-0.02150.1480.0778-00.22980.03790.02720.15050.01370.236612.148323.5155134.1108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 74 )A5 - 74
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 103 )A75 - 103
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 128 )A104 - 128
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 181 )A129 - 181
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 230 )A182 - 230
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 299 )A231 - 299
7X-RAY DIFFRACTION7chain 'A' and (resid 300 through 329 )A300 - 329
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 74 )B5 - 74
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 128 )B75 - 128
10X-RAY DIFFRACTION10chain 'B' and (resid 129 through 164 )B129 - 164
11X-RAY DIFFRACTION11chain 'B' and (resid 165 through 230 )B165 - 230
12X-RAY DIFFRACTION12chain 'B' and (resid 231 through 282 )B231 - 282
13X-RAY DIFFRACTION13chain 'B' and (resid 283 through 329 )B283 - 329

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