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- PDB-7cud: Crystal structure of HID in the unbound form -

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Basic information

Entry
Database: PDB / ID: 7cud
TitleCrystal structure of HID in the unbound form
ComponentsAmino acid ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / Hemoglobin / Staphylococcus aureus / Hemoglobin binding protein / protein-protein interaction / Shr / heme acquisition
Function / homology
Function and homology information


Heme-binding protein Shr-like, Hb-interacting domain / Heme-binding protein Shr-like, Hb-interacting domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype ...Heme-binding protein Shr-like, Hb-interacting domain / Heme-binding protein Shr-like, Hb-interacting domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain.
Similarity search - Domain/homology
BROMIDE ION / Heme-binding protein Shr
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCaaveiro, J.M.M. / Hoshino, M. / Tsumoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K06962 Japan
CitationJournal: To Be Published
Title: Structural basis for the recognition of human hemoglobin by the Shr protein from Streptococcus pyogenes
Authors: Caaveiro, J.M.M. / Hoshino, M. / Senoo, A. / Nakakido, M. / Nagatoishi, S. / Tame, J.R.H. / Tsumoto, K.
History
DepositionAug 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7822
Polymers13,7021
Non-polymers801
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.070, 76.070, 33.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-301-

BR

21A-435-

HOH

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Components

#1: Protein Amino acid ABC transporter substrate-binding protein / DUF1533 domain-containing protein / Heme-binding protein Shr


Mass: 13702.384 Da / Num. of mol.: 1 / Fragment: HID2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria)
Gene: shr, inlA_2, G3M98_06270, GTK50_07335, SAMEA3919037_01262
Production host: Escherichia coli (E. coli) / References: UniProt: B0LFQ8
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG-MME 2000 (20% w/v), 150mM KBr, 20mM TRIS-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→32.9 Å / Num. obs: 10571 / % possible obs: 99.8 % / Redundancy: 10.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1545 / CC1/2: 0.907

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DKQ

6dkq


Resolution: 1.8→30.18 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.543 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 435 4.1 %RANDOM
Rwork0.1547 ---
obs0.1569 10132 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.81 Å2 / Biso mean: 15.308 Å2 / Biso min: 8.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.8→30.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 1 114 1010
Biso mean--33.63 23.57 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013927
X-RAY DIFFRACTIONr_bond_other_d0.0010.017881
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.6351257
X-RAY DIFFRACTIONr_angle_other_deg1.4591.5882065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7195123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25726.4139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95815180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.162151
X-RAY DIFFRACTIONr_chiral_restr0.0850.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02163
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 20 -
Rwork0.174 768 -
all-788 -
obs--100 %

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