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- PDB-5wi5: 2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosam... -

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Basic information

Entry
Database: PDB / ID: 5wi5
Title2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium.
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid / (2R)-2-(phosphonooxy)propanoic acid / Magnesium
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / cytoplasm
Similarity search - Function
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
(2R)-2-(phosphonooxy)propanoic acid / Chem-EPU / UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric ...Title: 2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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 / struct_ncs_dom_lim
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 / _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

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,26316
Polymers184,7764
Non-polymers3,48712
Water11,476637
1
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0664
Polymers46,1941
Non-polymers8723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0664
Polymers46,1941
Non-polymers8723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0664
Polymers46,1941
Non-polymers8723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0664
Polymers46,1941
Non-polymers8723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1328
Polymers92,3882
Non-polymers1,7446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-25 kcal/mol
Surface area29280 Å2
MethodPISA
6
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1328
Polymers92,3882
Non-polymers1,7446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-28 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.243, 80.130, 126.511
Angle α, β, γ (deg.)90.00, 95.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA1 - 4224 - 425
21ALAALABB1 - 4224 - 425
12ILEILEAA1 - 4204 - 423
22ILEILECC1 - 4204 - 423
13ALAALAAA1 - 4224 - 425
23ALAALADD1 - 4224 - 425
14ILEILEBB1 - 4204 - 423
24ILEILECC1 - 4204 - 423
15ALAALABB1 - 4224 - 425
25ALAALADD1 - 4224 - 425
16ILEILECC1 - 4204 - 423
26ILEILEDD1 - 4204 - 423

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1 / Enoylpyruvate transferase 1 / UDP-N-acetylglucosamine enolpyruvyl transferase 1 / EPT 1


Mass: 46194.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: murA1, murA, SP_1966 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic
References: UniProt: Q97NQ4, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical
ChemComp-0V5 / (2R)-2-(phosphonooxy)propanoic acid


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EPU / URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID / ENOLPYRUVYL-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 677.400 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H29N3O19P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 8.2 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (B4), 0.01M MIB buffer (pH 7.0), 25% (w/v) PEG 1500.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 113220 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.04 / Rsym value: 0.076 / Χ2: 1.008 / Net I/σ(I): 18.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 5600 / CC1/2: 0.697 / Rpim(I) all: 0.405 / Rsym value: 0.756 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SG1

3sg1


Resolution: 2→29.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.668 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26625 5833 5.2 %RANDOM
Rwork0.22225 ---
obs0.22457 107143 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.996 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å20.14 Å2
2---2.21 Å20 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 2→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12687 0 220 637 13544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913195
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212752
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.98717894
X-RAY DIFFRACTIONr_angle_other_deg0.886329511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.03651705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21424.712520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.922152323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9771576
X-RAY DIFFRACTIONr_chiral_restr0.0880.22144
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0214585
X-RAY DIFFRACTIONr_gen_planes_other0.020.022403
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_it4.8075.0016799
X-RAY DIFFRACTIONr_mcbond_other4.80856798
X-RAY DIFFRACTIONr_mcangle_it6.7677.4758511
X-RAY DIFFRACTIONr_mcangle_other6.7677.4768512
X-RAY DIFFRACTIONr_scbond_it4.7195.3666396
X-RAY DIFFRACTIONr_scbond_other4.7195.3666395
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0677.8919384
X-RAY DIFFRACTIONr_long_range_B_refined9.51759.49414315
X-RAY DIFFRACTIONr_long_range_B_other9.52359.52514192
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)
11A265600.08
12B265600.08
21A261300.08
22C261300.08
31A265680.07
32D265680.07
41B256780.1
42C256780.1
51B258400.09
52D258400.09
61C257580.08
62D257580.08
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 425 -
Rwork0.301 7624 -
obs--96.88 %

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