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- PDB-6ckm: N. meningitidis CMP-sialic acid synthetase in the presence of CMP... -

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Basic information

Entry
Database: PDB / ID: 6ckm
TitleN. meningitidis CMP-sialic acid synthetase in the presence of CMP-sialic acid and Ca2+
ComponentsN-acylneuraminate cytidylyltransferase
KeywordsTRANSFERASE / polysaccharide synthesis / sialic acid-activator / CMP-transferase
Function / homology
Function and homology information


N-acylneuraminate cytidylyltransferase / N-acylneuraminate cytidylyltransferase activity / cytoplasm
Similarity search - Function
Acylneuraminate cytidylyltransferase / Cytidylyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-NCC / N-acylneuraminate cytidylyltransferase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.543 Å
AuthorsMatthews, M.M. / Fisher, A.J. / Chen, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI130684 United States
CitationJournal: Biochemistry / Year: 2019
Title: Catalytic Cycle ofNeisseria meningitidisCMP-Sialic Acid Synthetase Illustrated by High-Resolution Protein Crystallography.
Authors: Matthews, M.M. / McArthur, J.B. / Li, Y. / Yu, H. / Chen, X. / Fisher, A.J.
History
DepositionFeb 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6674
Polymers24,9201
Non-polymers7473
Water5,459303
1
A: N-acylneuraminate cytidylyltransferase
hetero molecules

A: N-acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3348
Polymers49,8412
Non-polymers1,4936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area5150 Å2
ΔGint-47 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.372, 156.020, 38.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-808-

HOH

21A-1030-

HOH

31A-1052-

HOH

41A-1060-

HOH

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Components

#1: Protein N-acylneuraminate cytidylyltransferase / / CMP-N-acetylneuraminic acid synthase / CMP-NeuNAc synthase / CMP-sialic acid synthase


Mass: 24920.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: neuA, siaB, synB / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A0Z8, N-acylneuraminate cytidylyltransferase
#2: Chemical ChemComp-NCC / CYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID


Mass: 614.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31N4O16P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.75 Å3/Da / Density % sol: 55.28 % / Description: long rectangular prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16M calcium acetate, 0.08M sodium cacodylate pH 6.5, 14.4% PEG 8000, and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.54→80.13 Å / Num. obs: 41624 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.86
Reflection shellResolution: 1.54→1.58 Å / Redundancy: 3.39 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.52 / Num. unique obs: 2739 / CC1/2: 0.798 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYR

1eyr


Resolution: 1.543→39.005 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.03
RfactorNum. reflection% reflection
Rfree0.1763 2097 5.04 %
Rwork0.1528 --
obs0.154 41623 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.543→39.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 48 303 2062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061799
X-RAY DIFFRACTIONf_angle_d0.7632449
X-RAY DIFFRACTIONf_dihedral_angle_d14.1851106
X-RAY DIFFRACTIONf_chiral_restr0.054292
X-RAY DIFFRACTIONf_plane_restr0.005316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5428-1.57870.2621270.21842280X-RAY DIFFRACTION87
1.5787-1.61820.23661430.19582674X-RAY DIFFRACTION100
1.6182-1.66190.19211200.18292606X-RAY DIFFRACTION100
1.6619-1.71080.19541410.1772636X-RAY DIFFRACTION100
1.7108-1.7660.17591540.15952629X-RAY DIFFRACTION100
1.766-1.82920.1831270.1652648X-RAY DIFFRACTION100
1.8292-1.90240.171390.15972628X-RAY DIFFRACTION100
1.9024-1.9890.20171560.14912629X-RAY DIFFRACTION99
1.989-2.09380.15151280.15032649X-RAY DIFFRACTION99
2.0938-2.2250.15751520.14932634X-RAY DIFFRACTION99
2.225-2.39680.18481430.14342658X-RAY DIFFRACTION99
2.3968-2.63790.16311390.1492644X-RAY DIFFRACTION99
2.6379-3.01950.18661470.15282667X-RAY DIFFRACTION99
3.0195-3.80380.17181330.14182716X-RAY DIFFRACTION99
3.8038-39.01750.16511480.14692828X-RAY DIFFRACTION99
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)
15.0536-0.60620.62815.7788-0.59835.0495-0.0318-0.3635-0.08680.3284-0.03290.01990.21930.0415-0.04590.1179-0.02880.01590.1341-0.01660.104520.863183.43437.2661
24.8771-1.39061.56313.8729-0.58283.45170.13420.0922-0.18470.0178-0.0267-0.51730.39530.5367-0.03510.12820.02420.00320.1762-0.02080.227132.9804178.21162.4325
31.20190.34550.11981.56880.3691.07540.0487-0.0844-0.0230.1047-0.0254-0.09960.04440.0473-0.01650.0866-0.006-0.0010.09160.02030.088921.4551183.28385.4058
48.7125-5.56350.0437.77050.41761.79170.05440.16590.4679-0.2844-0.1086-0.24390.0475-0.07760.09010.1259-0.01820.00450.1150.02310.112710.0732175.7668-5.5006
54.40350.51770.68784.29920.18313.6192-0.0519-0.38820.00880.25650.06110.0722-0.00210.0009-0.00110.19920.02530.00560.13590.00950.15158.7912149.72221.9034
61.4991-1.86941.34144.6752-4.96315.82020.09950.3013-0.0079-1.1892-0.3909-0.72930.3710.38290.19820.35240.00470.08340.2420.00860.203111.2131150.6783-10.9915
70.99050.1057-0.16471.37360.25991.01030.0014-0.0598-0.0545-0.0254-0.01290.06860.1144-0.04710.01670.1153-0.0105-0.00750.11910.00940.12212.0885174.3173-0.4691
85.408-0.99593.52972.692-0.36567.89580.1207-0.037-0.39090.45210.1696-0.80140.43210.3645-0.1870.29490.0927-0.04490.19790.00250.383131.3195165.96150.697
95.22460.42411.09513.85460.19048.03610.08820.880.0853-0.6175-0.1459-0.37410.12270.39670.07540.31770.21970.0030.5452-0.09010.616337.5571168.4552-6.3619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:16)
2X-RAY DIFFRACTION2(chain A and resid 17:43)
3X-RAY DIFFRACTION3(chain A and resid 44:123)
4X-RAY DIFFRACTION4(chain A and resid 124:135)
5X-RAY DIFFRACTION5(chain A and resid 136:160)
6X-RAY DIFFRACTION6(chain A and resid 161:170)
7X-RAY DIFFRACTION7(chain A and resid 171:203)
8X-RAY DIFFRACTION8(chain A and resid 204:217)
9X-RAY DIFFRACTION9(chain A and resid 218:225)

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