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

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Basic information

Entry
Database: PDB / ID: 6ckl
TitleN. meningitidis CMP-sialic acid synthetase in the presence of CMP and Neu5Ac2en
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
CYTIDINE-5'-MONOPHOSPHATE / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / CITRATE ANION / N-acylneuraminate cytidylyltransferase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.684 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 1.4Jul 29, 2020Group: Data collection / Derived calculations / Refinement description
Category: chem_comp / refine_hist ...chem_comp / refine_hist / struct_site / struct_site_gen
Item: _chem_comp.type / _refine_hist.d_res_high / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Assembly

Deposited unit
A: N-acylneuraminate cytidylyltransferase
B: N-acylneuraminate cytidylyltransferase
C: N-acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,08914
Polymers74,7613
Non-polymers2,32811
Water2,000111
1
A: N-acylneuraminate cytidylyltransferase
B: N-acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3309
Polymers49,8412
Non-polymers1,4897
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-43 kcal/mol
Surface area18850 Å2
MethodPISA
2
C: N-acylneuraminate cytidylyltransferase
hetero molecules

C: N-acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,51910
Polymers49,8412
Non-polymers1,6788
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7370 Å2
ΔGint-43 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.480, 151.010, 84.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 1 - 225 / Label seq-ID: 1 - 225

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

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


Mass: 24920.408 Da / Num. of mol.: 3
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
#4: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H17NO8

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Non-polymers , 4 types, 119 molecules

#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.68 Å3/Da / Density % sol: 54.06 % / Description: thick needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate/citric acid pH 5.5 and 20% PEG 3000
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.68→97.86 Å / Num. obs: 22814 / % possible obs: 97.1 % / Redundancy: 3.14 % / CC1/2: 0.995 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.57
Reflection shellResolution: 2.68→2.75 Å / Redundancy: 2.78 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 1615 / CC1/2: 0.727 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYR

1eyr


Resolution: 2.684→97.86 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU B: 12.529 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R Free: 0.334 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24171 1118 4.9 %RANDOM
Rwork0.1944 ---
obs0.19673 21689 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.447 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2---2 Å20 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 2.684→97.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5166 0 152 111 5429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195409
X-RAY DIFFRACTIONr_bond_other_d0.0060.025231
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9967343
X-RAY DIFFRACTIONr_angle_other_deg1.24312056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88325.197229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69915933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1761528
X-RAY DIFFRACTIONr_chiral_restr0.0820.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216090
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021175
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8124.1962699
X-RAY DIFFRACTIONr_mcbond_other2.8134.1952698
X-RAY DIFFRACTIONr_mcangle_it4.4586.293369
X-RAY DIFFRACTIONr_mcangle_other4.4586.2923370
X-RAY DIFFRACTIONr_scbond_it2.9594.5332710
X-RAY DIFFRACTIONr_scbond_other2.9574.5322708
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7346.6573973
X-RAY DIFFRACTIONr_long_range_B_refined6.9232.3675730
X-RAY DIFFRACTIONr_long_range_B_other6.9232.3745731
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A276240.07
12B276240.07
21A278320.06
22C278320.06
31B277560.06
32C277560.06
LS refinement shellResolution: 2.684→2.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 67 -
Rwork0.294 1545 -
obs--94.21 %

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