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- PDB-7kpz: 1.70 A resolution crystal structure of Group A Streptococcus HupZ... -

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Basic information

Entry
Database: PDB / ID: 7kpz
Title1.70 A resolution crystal structure of Group A Streptococcus HupZ-V5-His6
ComponentsHupZ
KeywordsOXIDOREDUCTASE / heme degradation / heme binding protein / enzyme
Function / homologyPyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / FMN-binding split barrel / Pyridoxamine 5'-phosphate oxidase N-terminal domain-containing protein
Function and homology information
Biological speciesStreptococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsLi, J. / Liu, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01CA247379 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
CitationJournal: Molecules / Year: 2021
Title: Heme Binding to HupZ with a C-Terminal Tag from Group A Streptococcus.
Authors: Traore, E.S. / Li, J. / Chiura, T. / Geng, J. / Sachla, A.J. / Yoshimoto, F. / Eichenbaum, Z. / Davis, I. / Mak, P.J. / Liu, A.
History
DepositionNov 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HupZ
B: HupZ


Theoretical massNumber of molelcules
Total (without water)37,0062
Polymers37,0062
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, DIMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-10 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.020, 62.378, 94.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HupZ / Pyridoxamine 5'-phosphate oxidase


Mass: 18502.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria) / Gene: MGAS10270_Spy0711 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9A0B9*PLUS, pyridoxal 5'-phosphate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.6 Å3/Da / Density % sol: 23.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 20% PEG3350, 0.2 M lithium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97913 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 26686 / % possible obs: 99.7 % / Redundancy: 9.7 % / Biso Wilson estimate: 22.75 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.02 / Rrim(I) all: 0.062 / Χ2: 0.975 / Net I/σ(I): 10.8 / Num. measured all: 258352
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.739.90.18313320.9860.0610.1930.54199.9
1.73-1.76100.16612970.9880.0550.1750.54399.5
1.76-1.79100.15513120.9890.0510.1630.57599.8
1.79-1.839.80.13913160.990.0460.1460.62499.8
1.83-1.879.90.12613040.9910.0420.1330.67299.8
1.87-1.919.50.13113140.9930.0430.1380.74299.8
1.91-1.968.80.112980.9930.0350.1060.80799.4
1.96-2.02100.09613410.9950.0320.1010.88799.9
2.02-2.0710.10.0913120.9940.030.0950.90799.8
2.07-2.14100.08413240.9960.0280.0890.95199.8
2.14-2.229.80.08113270.9950.0270.0851.00699.8
2.22-2.319.50.07713200.9950.0260.0821.09399.5
2.31-2.419.10.07313190.9950.0260.0771.07899.8
2.41-2.5410.10.0713220.9980.0230.0731.07899.8
2.54-2.7100.06813510.9970.0230.0721.16199.6
2.7-2.919.80.06313280.9980.0210.0671.2399.9
2.91-3.29.20.05713470.9970.020.0611.29599.6
3.2-3.66100.05413860.9970.0180.0571.39699.9
3.66-4.619.10.04913660.9980.0170.0521.31599.3
4.61-509.10.04914700.9980.0170.0521.55899.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.9refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5ESC

5esc


Resolution: 1.703→37.761 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 1998 7.5 %
Rwork0.1836 24635 -
obs0.1863 26633 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.58 Å2 / Biso mean: 28.1544 Å2 / Biso min: 14.18 Å2
Refinement stepCycle: final / Resolution: 1.703→37.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 0 208 2187
Biso mean---34.66 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072009
X-RAY DIFFRACTIONf_angle_d1.0562703
X-RAY DIFFRACTIONf_chiral_restr0.043291
X-RAY DIFFRACTIONf_plane_restr0.004357
X-RAY DIFFRACTIONf_dihedral_angle_d14.674761
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.703-1.74530.22031380.1875170197
1.7453-1.79250.24931390.18941715100
1.7925-1.84520.24321420.18631744100
1.8452-1.90480.23981420.1971750100
1.9048-1.97280.24141390.17641710100
1.9728-2.05180.21191400.18531726100
2.0518-2.14520.2251450.18871778100
2.1452-2.25830.21071390.18311742100
2.2583-2.39980.22711430.18191750100
2.3998-2.5850.22061430.21081767100
2.585-2.84510.2391440.20411778100
2.8451-3.25660.25231440.19581774100
3.2566-4.10210.18661470.171812100
4.1021-37.7610.20461530.1687188899

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