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- PDB-5jp9: Crystal Structure of cytidine monophosphate hydroxymethylase MilA... -

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Basic information

Entry
Database: PDB / ID: 5jp9
TitleCrystal Structure of cytidine monophosphate hydroxymethylase MilA with dCMP
ComponentsCMP 5-hydroxymethylase
KeywordsTRANSFERASE / CMP hydroxymethylase
Function / homology
Function and homology information


thymidylate synthase activity / dTMP biosynthetic process / methylation / cytosol
Similarity search - Function
Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / CMP 5-hydroxymethylase
Similarity search - Component
Biological speciesStreptomyces rimofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 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
DepositionMay 3, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)73,6704
Polymers73,0562
Non-polymers6142
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-25 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.298, 109.298, 113.155
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-697-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 5:10 or (resid 11 and (name...
21(chain B and (resseq 5:10 or (resid 11 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLNGLN(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 101 - 6
12ASPASPASPASP(chain A and (resseq 5:10 or (resid 11 and (name...AA117
13THRTHRGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 3291 - 325
14THRTHRGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 3291 - 325
15THRTHRGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 3291 - 325
16THRTHRGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 3291 - 325
17THRTHRGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 3291 - 325
18THRTHRGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 3291 - 325
21THRTHRGLNGLN(chain B and (resseq 5:10 or (resid 11 and (name...BB5 - 101 - 6
22ASPASPASPASP(chain B and (resseq 5:10 or (resid 11 and (name...BB117
23THRTHRGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB5 - 3291 - 325
24THRTHRGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB5 - 3291 - 325
25THRTHRGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB5 - 3291 - 325
26THRTHRGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB5 - 3291 - 325
27THRTHRGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB5 - 3291 - 325
28THRTHRGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB5 - 3291 - 325

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Components

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


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-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
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: 2.1→50 Å / Num. obs: 44002 / % possible obs: 95.8 % / Redundancy: 11 % / Biso Wilson estimate: 20.67 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.037 / Rrim(I) all: 0.124 / Χ2: 1 / Net I/av σ(I): 17.824 / Net I/σ(I): 8.8 / Num. measured all: 484354
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1811.30.32945080.970.1020.3440.998100
2.18-2.2610.40.32630770.9740.1040.3420.99868.1
2.26-2.3711.10.24145750.9850.0750.2530.999100
2.37-2.4911.30.18745480.9890.0580.1961.001100
2.49-2.6511.30.15845420.9930.0490.1651.001100
2.65-2.8511.20.16845800.9860.0520.1760.997100
2.85-3.1411.30.1245980.9940.0370.1251.001100
3.14-3.5911.20.13345840.9880.0420.141.003100
3.59-4.5210.10.08541730.9950.0280.090.99789.6
4.52-5010.80.05948170.9970.0190.0621.00299.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JNH

5jnh


Resolution: 2.101→49.21 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.21
RfactorNum. reflection% reflection
Rfree0.2063 2159 4.92 %
Rwork0.155 --
obs0.1574 43870 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.42 Å2 / Biso mean: 21.5548 Å2 / Biso min: 6.19 Å2
Refinement stepCycle: final / Resolution: 2.101→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5079 0 40 501 5620
Biso mean--16.26 31.62 -
Num. residues----635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075263
X-RAY DIFFRACTIONf_angle_d0.8627165
X-RAY DIFFRACTIONf_chiral_restr0.067751
X-RAY DIFFRACTIONf_plane_restr0.006943
X-RAY DIFFRACTIONf_dihedral_angle_d14.2343048
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2767X-RAY DIFFRACTION5.23TORSIONAL
12B2767X-RAY DIFFRACTION5.23TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1014-2.15020.24061250.155328572982100
2.1502-2.2040.2221580.151928813039100
2.204-2.26360.2513700.22841446151651
2.2636-2.33020.27071550.1682834298998
2.3302-2.40540.21281510.148228723023100
2.4054-2.49140.20431790.145828803059100
2.4914-2.59110.2131500.152328763026100
2.5911-2.70910.20911620.150628813043100
2.7091-2.85190.19971630.154628773040100
2.8519-3.03050.21461340.154729383072100
3.0305-3.26450.20741460.156728903036100
3.2645-3.59290.20381490.153529283077100
3.5929-4.11260.20361240.15342482260684
4.1126-5.18050.16241310.132929913122100
5.1805-49.22390.20311620.177130783240100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2596-0.00750.07280.04030.020.10030.0870.22890.0270.0102-0.1218-0.0898-0.04650.0658-0.00760.14490.02250.01810.162-0.00150.086672.543528.165999.7804
20.0024-0.0025-0.0062-0.00250.012-0.00010.0391-0.0567-0.06950.0329-0.1286-0.0536-0.06160.0593-0.00020.0633-0.01-0.01210.1420.02560.107882.462624.5094113.9999
30.5284-0.0746-0.21440.1737-0.10070.22090.1468-0.5613-0.10410.1408-0.1037-0.0396-0.02560.12190.01220.0832-0.029-0.02040.17980.01940.083771.340623.5661123.977
40.2722-0.0422-0.07320.01280.00140.07650.0781-0.1807-0.06710.0443-0.1474-0.0307-0.0064-0.0025-0.00740.1152-0.0217-0.01410.1209-0.0110.118661.627621.5996116.5185
50.2852-0.0770.03880.09980.00880.1380.06030.064-0.0655-0.03-0.0918-0.0369-0.03040.13610.00020.09110.00690.00820.11320.00420.109373.349222.5783107.1315
60.48740.25610.08510.2396-0.08340.21550.2172-0.4693-0.58070.1005-0.1169-0.42320.10260.09270.03890.09030.0139-0.0270.24310.1260.226488.708814.2118122.665
70.04040.0303-0.02510.51080.23030.14070.0023-0.1099-0.1046-0.1295-0.0119-0.2186-0.02630.1192-0.01460.08230.00110.00190.21050.03860.178795.124821.8692114.9833
80.34360.2740.10540.10730.10310.0561-0.08410.1305-0.0971-0.04880.0611-0.0027-0.0122-0.0286-0.00140.11560.0130.01130.1123-0.01330.097446.848515.982899.0361
90.0259-0.00290.04120.03710.00670.03130.0448-0.12340.07180.157-0.05190.1584-0.0415-0.10370.00010.11640.0116-0.00310.11210.00840.124837.112815.4979118.1105
100.0251-0.0087-0.01770.04620.03070.06150.0447-0.12610.0569-0.03110.0417-0.02350.01330.0828-00.1342-0.00470.01330.1381-0.00430.133349.559932.3486118.5349
110.6104-0.0289-0.21480.0560.21840.17850.02430.0692-0.0328-0.0206-0.04810.0182-0.0044-0.0279-0.00070.1002-0.00070.00220.07850.0070.067250.036222.4267106.6303
120.17340.09320.00480.06530.0060.0439-0.0284-0.00910.0239-0.04210.02060.0355-0.0162-0.03790.08610.08420.0416-0.01120.08930.00360.105627.456929.6254107.7162
130.02050.00140.03330.03760.01830.03720.09990.2664-0.1607-0.0416-0.02490.23080.0424-0.20200.15960.0222-0.04190.2089-0.00640.203323.36620.112898.5863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 55 )A5 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 73 )A56 - 73
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 128 )A74 - 128
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 164 )A129 - 164
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 230 )A165 - 230
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 282 )A231 - 282
7X-RAY DIFFRACTION7chain 'A' and (resid 283 through 329 )A283 - 329
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 73 )B5 - 73
9X-RAY DIFFRACTION9chain 'B' and (resid 74 through 103 )B74 - 103
10X-RAY DIFFRACTION10chain 'B' and (resid 104 through 128 )B104 - 128
11X-RAY DIFFRACTION11chain 'B' and (resid 129 through 230 )B129 - 230
12X-RAY DIFFRACTION12chain 'B' and (resid 231 through 299 )B231 - 299
13X-RAY DIFFRACTION13chain 'B' and (resid 300 through 329 )B300 - 329

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