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- PDB-6ckj: N. meningitidis CMP-sialic acid synthetase, ligand-free -

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Basic information

Entry
Database: PDB / ID: 6ckj
TitleN. meningitidis CMP-sialic acid synthetase, ligand-free
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
ACETATE ION / N-acylneuraminate cytidylyltransferase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 11, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)25,1195
Polymers24,9201
Non-polymers1984
Water4,414245
1
A: N-acylneuraminate cytidylyltransferase
hetero molecules

A: N-acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,23710
Polymers49,8412
Non-polymers3968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area3180 Å2
ΔGint-24 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.783, 155.056, 38.777
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-303-

CA

21A-304-

CA

31A-574-

HOH

41A-605-

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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 55.27 % / 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: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.75→38.78 Å / Num. obs: 27855 / % possible obs: 96 % / Redundancy: 3.43 % / CC1/2: 0.995 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.34 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1446 / CC1/2: 0.794 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYR

1eyr


Resolution: 1.75→38.777 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 17.08
RfactorNum. reflection% reflectionSelection details
Rfree0.1865 1405 5.05 %RANDOM
Rwork0.1571 ---
obs0.1586 27840 95.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→38.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 10 245 1969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061754
X-RAY DIFFRACTIONf_angle_d0.7512379
X-RAY DIFFRACTIONf_dihedral_angle_d11.891078
X-RAY DIFFRACTIONf_chiral_restr0.054281
X-RAY DIFFRACTIONf_plane_restr0.004314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.8120.23781300.19812574X-RAY DIFFRACTION94
1.812-1.88460.20721300.18512634X-RAY DIFFRACTION97
1.8846-1.97030.24751540.1742641X-RAY DIFFRACTION97
1.9703-2.07420.20061300.16492643X-RAY DIFFRACTION97
2.0742-2.20410.19191340.15432398X-RAY DIFFRACTION87
2.2041-2.37430.19211540.15082676X-RAY DIFFRACTION98
2.3743-2.61320.181480.15422715X-RAY DIFFRACTION99
2.6132-2.99120.17311480.15982724X-RAY DIFFRACTION98
2.9912-3.76810.19011340.14752692X-RAY DIFFRACTION96
3.7681-38.78650.15731430.1492738X-RAY DIFFRACTION93
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)
10.55680.72510.32510.78310.64390.50520.05180.0573-0.05750.11070.0246-0.20210.13190.05940.01680.06930.0141-0.01660.07990.00810.093328.0576179.32574.409
20.96780.6319-0.01020.94380.22420.46340.0647-0.0548-0.03530.0692-0.0432-0.08060.03710.02860.01390.0741-0.0028-0.00770.0740.02450.062719.9171180.92914.072
30.3289-0.1334-0.01250.5415-0.04770.1721-0.06-0.1095-0.0633-0.1003-0.002-0.01210.04740.0855-0.00040.1624-0.00330.01140.07260.02240.07179.6811150.2371-2.0226
40.22690.29510.16870.3564-0.06220.45060.0429-0.0694-0.0782-0.0471-0.00310.01460.06560.041300.0601-0.00260.00040.05740.010.079114.436172.9905-0.5766
50.0250.04830.04880.14670.10440.07550.30160.1797-0.12560.32380.3105-0.32630.38150.11390.0026-0.03510.4429-0.24980.1508-0.04210.626935.9408165.7816-0.7177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:43))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 44:136))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 137:174))
4X-RAY DIFFRACTION4chain 'A' and ((resseq 175:209))
5X-RAY DIFFRACTION5chain 'A' and ((resseq 210:225))

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