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- PDB-4hmp: Crystal structure of iron uptake ABC transporter substrate-bindin... -

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Basic information

Entry
Database: PDB / ID: 4hmp
TitleCrystal structure of iron uptake ABC transporter substrate-binding protein PiaA from Streptococcus pneumoniae TIGR4
ComponentsIron-compound ABC transporter, iron compound-binding protein
KeywordsTRANSPORT PROTEIN / class III substrate binding protein / alpha and beta protein / periplasmic binding protein type III fold / iron uptake ABC transporter system substrate-binding protein / hydroxamate siderophore / membrane-anchored lipoprotein
Function / homology
Function and homology information


: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Iron-compound ABC transporter, iron compound-binding protein / Iron-compound ABC transporter, iron compound-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsCheng, W. / Li, Q. / Jiang, Y.-L. / Chen, Y. / Zhou, C.-Z.
CitationJournal: Plos One / Year: 2013
Title: Structures of Streptococcus pneumoniae PiaA and Its Complex with Ferrichrome Reveal Insights into the Substrate Binding and Release of High Affinity Iron Transporters
Authors: Cheng, W. / Li, Q. / Jiang, Y.-L. / Zhou, C.-Z. / Chen, Y.
History
DepositionOct 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-compound ABC transporter, iron compound-binding protein
B: Iron-compound ABC transporter, iron compound-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,11938
Polymers73,0292
Non-polymers4,08936
Water1,42379
1
A: Iron-compound ABC transporter, iron compound-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,61120
Polymers36,5151
Non-polymers2,09719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron-compound ABC transporter, iron compound-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,50718
Polymers36,5151
Non-polymers1,99317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.037, 86.299, 93.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 263 - 265 / Label seq-ID: 250 - 252

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Iron-compound ABC transporter, iron compound-binding protein


Mass: 36514.586 Da / Num. of mol.: 2 / Fragment: UNP residues 23-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1032 / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL(DE3) / References: UniProt: Q97R09, UniProt: A0A0H2UPT5*PLUS

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Non-polymers , 5 types, 115 molecules

#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.2
Details: 30% PEG 400, 0.1M NaAc, 0.1M CdCl2, pH 5.2, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97908 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 17106 / Num. obs: 17491 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.2 / Num. unique all: 826 / Rsym value: 0.245 / % possible all: 97.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→41.12 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.876 / Occupancy max: 1 / Occupancy min: 0 / SU B: 12.478 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29747 861 5 %RANDOM
Rwork0.25345 ---
obs0.25562 16211 97.85 %-
all-16568 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.7 Å2 / Biso mean: 27.867 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2---0.25 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 71 79 4593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224534
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8661.9846132
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2795572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9826.322174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88815799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.579158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213288
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4761.52876
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79724623
X-RAY DIFFRACTIONr_scbond_it0.46831658
X-RAY DIFFRACTIONr_scangle_it0.8274.51509
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 24 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.30.05
tight thermal0.450.5
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 67 -
Rwork0.265 1148 -
obs--97.04 %

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