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- PDB-5w56: Structure of Apo AztC -

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Basic information

Entry
Database: PDB / ID: 5w56
TitleStructure of Apo AztC
ComponentsPeriplasmic solute binding protein
KeywordsMETAL BINDING PROTEIN / Solute binding protein / Zinc / ABC Transporter
Function / homology
Function and homology information


zinc ion transport / periplasmic space / cell adhesion / zinc ion binding
Similarity search - Function
: / Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
High-affinity zinc uptake system protein AztC
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsAvalos, D. / Yukl, E.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1SC2GM111170-01 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Mechanisms of zinc binding to the solute-binding protein AztC and transfer from the metallochaperone AztD.
Authors: Neupane, D.P. / Avalos, D. / Fullam, S. / Roychowdhury, H. / Yukl, E.T.
History
DepositionJun 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic solute binding protein
B: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0978
Polymers59,6832
Non-polymers4146
Water2,450136
1
A: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0484
Polymers29,8411
Non-polymers2073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0484
Polymers29,8411
Non-polymers2073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.469, 106.261, 61.672
Angle α, β, γ (deg.)90.00, 110.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic solute binding protein


Mass: 29841.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: Pden_1597 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A1B2F3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 292 K / Method: batch mode / pH: 7 / Details: Sodium formate 4.0-4.5 M, Bis-tris propane 0.1 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.03→45.83 Å / Num. obs: 47607 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.016 / Net I/σ(I): 20.3
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3532 / CC1/2: 0.805 / Rpim(I) all: 0.34 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Aimlessv0.5.32data scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XRV

4xrv
PDB Unreleased entry


Resolution: 2.03→45.83 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 7.255 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20085 2008 4.2 %RANDOM
Rwork0.16533 ---
obs0.16681 45559 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.757 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20.49 Å2
2--1.95 Å20 Å2
3----1.34 Å2
Refinement stepCycle: 1 / Resolution: 2.03→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 0 26 136 4143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194105
X-RAY DIFFRACTIONr_bond_other_d0.0010.023873
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.9475597
X-RAY DIFFRACTIONr_angle_other_deg0.9563.0018829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08723.548186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91115571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.711533
X-RAY DIFFRACTIONr_chiral_restr0.130.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02953
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 150 -
Rwork0.295 3377 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3043-0.1998-0.31750.5890.25390.7412-0.0439-0.00240.07120.06220.00750.04790.1730.05890.03640.07520.06680.01380.0965-0.00360.07258.94242.04469.7161
20.53260.3924-0.05690.73260.02990.2375-0.08960.0530.0715-0.00830.00170.0532-0.01390.01620.08790.0524-0.049-0.02710.1180.05740.07148.80442.331721.4768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 309
2X-RAY DIFFRACTION2B26 - 309

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