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

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Basic information

Entry
Database: PDB / ID: 6ckk
TitleN. meningitidis CMP-sialic acid synthetase in the presence of CTP 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
CYTIDINE-5'-TRIPHOSPHATE / N-acylneuraminate cytidylyltransferase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,9277
Polymers49,8412
Non-polymers1,0875
Water12,250680
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-52 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.190, 69.560, 158.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2
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-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.32 Å3/Da / Density % sol: 46.93 % / Description: rectangular
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M imidazole pH 8, 6% PEG 8000, and 0.2M calcium acetate
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.03316 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.8→79.11 Å / Num. obs: 42666 / % possible obs: 93.8 % / Redundancy: 3.35 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.64
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.56 / Num. unique obs: 2883 / CC1/2: 0.92 / % possible all: 87.7

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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: 1.8→79.11 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24958 2171 5.1 %RANDOM
Rwork0.2019 ---
obs0.20435 40429 93.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.468 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.54 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.8→79.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3441 0 61 680 4182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193638
X-RAY DIFFRACTIONr_bond_other_d0.0020.023528
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9874930
X-RAY DIFFRACTIONr_angle_other_deg1.02638090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95725.163153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57815632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3571519
X-RAY DIFFRACTIONr_chiral_restr0.1050.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214109
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02788
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_it1.9481.9581845
X-RAY DIFFRACTIONr_mcbond_other1.9281.9491840
X-RAY DIFFRACTIONr_mcangle_it3.0572.912300
X-RAY DIFFRACTIONr_mcangle_other3.062.9142301
X-RAY DIFFRACTIONr_scbond_it2.5642.3171793
X-RAY DIFFRACTIONr_scbond_other2.5632.3181794
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0013.3432631
X-RAY DIFFRACTIONr_long_range_B_refined7.64818.1064669
X-RAY DIFFRACTIONr_long_range_B_other7.57217.8674628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 133 -
Rwork0.239 2746 -
obs--87.59 %

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