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- PDB-6ifi: Crystal Structure of the Apo form of CMP-N-acetylneuraminate Synt... -

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Basic information

Entry
Database: PDB / ID: 6ifi
TitleCrystal Structure of the Apo form of CMP-N-acetylneuraminate Synthetase from Vibrio cholerae
ComponentsCMP-N-acetylneuraminate Synthetase
KeywordsSUGAR BINDING PROTEIN / Bacterial / CMP-sialic acid synthetase / sialic acid / CTP
Function / homologySpore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Alpha-Beta Complex / Alpha Beta
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBose, S. / Subramanian, R.
Funding support India, 3items
OrganizationGrant numberCountry
BT/IN/SWEDEN/06/SR/2017-2018) India
BT/PR5081/INF/156/2012 India
BT/PR12422/MED/31/287/214 India
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structural and functional characterization of CMP-N-acetylneuraminate synthetase from Vibrio cholerae.
Authors: Bose, S. / Purkait, D. / Joseph, D. / Nayak, V. / Subramanian, R.
History
DepositionSep 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: CMP-N-acetylneuraminate Synthetase
B: CMP-N-acetylneuraminate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0274
Polymers56,9472
Non-polymers802
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-27 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.250, 75.250, 109.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein CMP-N-acetylneuraminate Synthetase


Mass: 28473.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) / References: N-acylneuraminate cytidylyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 8000, calcium acetate, imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.8→47.87 Å / Num. obs: 14951 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.7
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 356 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZI

1ezi


Resolution: 2.8→25.08 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.881 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.749 / SU Rfree Blow DPI: 0.308 / SU Rfree Cruickshank DPI: 0.319
RfactorNum. reflection% reflectionSelection details
Rfree0.24 843 5.64 %RANDOM
Rwork0.212 ---
obs0.213 14951 99.2 %-
Displacement parametersBiso max: 124.23 Å2 / Biso mean: 64.35 Å2 / Biso min: 23.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.7015 Å20 Å20 Å2
2---0.7015 Å20 Å2
3---1.4029 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 2.8→25.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 2 66 3356
Biso mean--107.51 54.62 -
Num. residues----428
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1098SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes563HARMONIC5
X-RAY DIFFRACTIONt_it3362HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion468SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3776SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3362HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4586HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion19.4
LS refinement shellResolution: 2.8→2.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 42
RfactorNum. reflection% reflection
Rfree0.2969 24 6.74 %
Rwork0.2651 332 -
all0.2671 356 -
obs--87.25 %

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