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- PDB-8wmy: Crystal structure of YqeK in complex with MG and ADP. -

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Basic information

Entry
Database: PDB / ID: 8wmy
TitleCrystal structure of YqeK in complex with MG and ADP.
Componentsbis(5'-nucleosyl)-tetraphosphatase (symmetrical)
KeywordsHYDROLASE / Staphylococcus pyogenes / YqeK / Protein structure / enzymatic activity.
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / hydrolase activity / nucleotide binding / metal ion binding
Similarity search - Function
Ap4A hydrolase / : / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
Similarity search - Component
Biological speciesStaphylococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsMo, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071476 China
CitationJournal: To be published
Title: Molecular Mechanism of Ap4A Hydrolysis by YqeK of Staphylococcus pyogenes.
Authors: Mo, X.
History
DepositionOct 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
B: bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9278
Polymers44,9762
Non-polymers9526
Water5,603311
1
A: bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
hetero molecules

B: bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9278
Polymers44,9762
Non-polymers9526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3350 Å2
ΔGint-75 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.944, 37.672, 76.301
Angle α, β, γ (deg.)90.000, 92.704, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU(chain 'A' and (resid 2 through 195 or resid 201))AA2 - 1942 - 194
12ADPADPADPADP(chain 'A' and (resid 2 through 195 or resid 201))AC201
21THRTHRLEULEUchain 'B'BB2 - 1942 - 194
22ADPADPADPADPchain 'B'BF201

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Components

#1: Protein bis(5'-nucleosyl)-tetraphosphatase (symmetrical)


Mass: 22487.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Staphylococcus aureus is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A4U7IGH6.
Source: (gene. exp.) Staphylococcus (bacteria) / Gene: E0F66_02650, SAMEA1711581_00596, SAMEA864267_01112 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4U7IGH6, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 293.15 K / Method: evaporation
Details: 12% 2-propannol, 18.5% PEG-4000 and 100 mM sodium HEPES (pH 7.4)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→35.04 Å / Num. obs: 35345 / % possible obs: 98.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.17 Å2 / CC1/2: 0.98 / Net I/σ(I): 3
Reflection shellResolution: 1.91→1.978 Å / Num. unique obs: 3499 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→35.04 Å / SU ML: 0.2506 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.6335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 1767 5 %
Rwork0.2147 33577 -
obs0.2165 35344 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.8 Å2
Refinement stepCycle: LAST / Resolution: 1.91→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 58 311 3494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01383250
X-RAY DIFFRACTIONf_angle_d1.56124423
X-RAY DIFFRACTIONf_chiral_restr0.072497
X-RAY DIFFRACTIONf_plane_restr0.0109552
X-RAY DIFFRACTIONf_dihedral_angle_d13.8908449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.35281300.2912488X-RAY DIFFRACTION95.1
1.96-2.020.29951200.25392557X-RAY DIFFRACTION98.89
2.02-2.080.29931260.23822596X-RAY DIFFRACTION98.91
2.08-2.160.27661360.22252566X-RAY DIFFRACTION98.97
2.16-2.240.27991400.22162606X-RAY DIFFRACTION99.13
2.24-2.340.25481560.21922591X-RAY DIFFRACTION99.31
2.34-2.470.30631290.21882569X-RAY DIFFRACTION99.45
2.47-2.620.29011170.22552631X-RAY DIFFRACTION99.49
2.62-2.820.26681370.22392622X-RAY DIFFRACTION99.5
2.82-3.110.26611480.21912616X-RAY DIFFRACTION99.64
3.11-3.560.26741430.21112622X-RAY DIFFRACTION99.53
3.56-4.480.19751470.17872561X-RAY DIFFRACTION96.3
4.48-35.040.20541380.21982552X-RAY DIFFRACTION92.57

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