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- PDB-5esc: Crystal structure of Group A Streptococcus HupZ -

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Basic information

Entry
Database: PDB / ID: 5esc
TitleCrystal structure of Group A Streptococcus HupZ
ComponentsHupZ
KeywordsOXIDOREDUCTASE / Enzyme / Heme degredation / dimer / Split-barrel
Function / homologyPyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / Hypothetical cytosolic protein
Function and homology information
Biological speciesStreptococcus sp. 'group A' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAgniswamy, J. / Weber, I.T.
CitationJournal: Biometals / Year: 2016
Title: In vitro heme biotransformation by the HupZ enzyme from Group A streptococcus.
Authors: Sachla, A.J. / Ouattara, M. / Romero, E. / Agniswamy, J. / Weber, I.T. / Gadda, G. / Eichenbaum, Z.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Feb 13, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HupZ
B: HupZ
C: HupZ
D: HupZ


Theoretical massNumber of molelcules
Total (without water)59,8114
Polymers59,8114
Non-polymers00
Water4,864270
1
A: HupZ
B: HupZ


Theoretical massNumber of molelcules
Total (without water)29,9062
Polymers29,9062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-16 kcal/mol
Surface area11750 Å2
MethodPISA
2
C: HupZ
D: HupZ


Theoretical massNumber of molelcules
Total (without water)29,9062
Polymers29,9062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-13 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.823, 61.181, 61.347
Angle α, β, γ (deg.)78.59, 86.76, 80.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
HupZ / Hypothetical cytosolic protein


Mass: 14952.872 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group A' (bacteria) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q1JHG0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Lithium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 39089 / % possible obs: 98.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 7.69 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HTD

2htd


Resolution: 2→46.88 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.349 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20803 3898 10.1 %RANDOM
Rwork0.16658 ---
obs0.17078 34858 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.664 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å2-0.33 Å2-0.63 Å2
2---0.23 Å20.41 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 2→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 0 270 4082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193989
X-RAY DIFFRACTIONr_bond_other_d0.0050.023941
X-RAY DIFFRACTIONr_angle_refined_deg2.051.9465389
X-RAY DIFFRACTIONr_angle_other_deg1.11439033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6085504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06524.231208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60315763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1991538
X-RAY DIFFRACTIONr_chiral_restr0.1230.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024586
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02956
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_it2.0142.2161932
X-RAY DIFFRACTIONr_mcbond_other2.0132.2141931
X-RAY DIFFRACTIONr_mcangle_it2.9963.2942416
X-RAY DIFFRACTIONr_mcangle_other2.9963.2962417
X-RAY DIFFRACTIONr_scbond_it3.3592.7022057
X-RAY DIFFRACTIONr_scbond_other3.3582.7042058
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0493.8652958
X-RAY DIFFRACTIONr_long_range_B_refined7.03918.0044563
X-RAY DIFFRACTIONr_long_range_B_other6.95717.8694506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 284 -
Rwork0.176 2396 -
obs--91.41 %

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