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- PDB-6xpn: Z-loop Deletion Mutant of AztC from Paracoccus denitrificans -

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Basic information

Entry
Database: PDB / ID: 6xpn
TitleZ-loop Deletion Mutant of AztC from Paracoccus denitrificans
ComponentsPeriplasmic solute binding protein
KeywordsMETAL BINDING PROTEIN / zinc / solute binding protein / 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
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: 2.26 Å
AuthorsYukl, E.T.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122819
CitationJournal: Biomolecules / Year: 2020
Title: Structural Features Mediating Zinc Binding and Transfer in the AztABCD Zinc Transporter System.
Authors: Meni, A. / Yukl, E.T.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,3304
Polymers63,1992
Non-polymers1312
Water1,02757
1
B: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6652
Polymers31,6001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6652
Polymers31,6001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.292, 105.042, 64.245
Angle α, β, γ (deg.)90.000, 110.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 26 through 35 or resid 37 through 80 or resid 82 through 309))
21(chain B and (resid 26 through 35 or resid 37 through 80 or resid 82 through 309))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROILEILE(chain A and (resid 26 through 35 or resid 37 through 80 or resid 82 through 309))AB26 - 3526 - 35
12GLYGLYLEULEU(chain A and (resid 26 through 35 or resid 37 through 80 or resid 82 through 309))AB37 - 8037 - 80
13ASNASNARGARG(chain A and (resid 26 through 35 or resid 37 through 80 or resid 82 through 309))AB82 - 30982 - 301
21PROPROILEILE(chain B and (resid 26 through 35 or resid 37 through 80 or resid 82 through 309))BA26 - 3526 - 35
22GLYGLYLEULEU(chain B and (resid 26 through 35 or resid 37 through 80 or resid 82 through 309))BA37 - 8037 - 80
23ASNASNARGARG(chain B and (resid 26 through 35 or resid 37 through 80 or resid 82 through 309))BA82 - 30982 - 301

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Components

#1: Protein Periplasmic solute binding protein


Mass: 31599.514 Da / Num. of mol.: 2 / Mutation: deleted residues 222-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: Pden_1597 / Production host: Escherichia coli (E. coli) / References: UniProt: A1B2F3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7
Details: Protein at 26 mg/mL was combined in a 1:1 ratio with crystallization solution containing 0.1 M bis-tris propane pH 7.0 and 4.1 M sodium formate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2020
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→46.63 Å / Num. obs: 36075 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 58.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.021 / Rrim(I) all: 0.042 / Net I/σ(I): 18.5 / Num. measured all: 133590 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.26-2.333.70.5891222533230.840.3530.6892.399.9
9.04-46.633.50.02520115750.9990.0150.02947.396.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W57

5w57


Resolution: 2.26→39.54 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 2011 5.58 %
Rwork0.1735 34021 -
obs0.1754 36032 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.52 Å2 / Biso mean: 67.5133 Å2 / Biso min: 35.45 Å2
Refinement stepCycle: final / Resolution: 2.26→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 2 57 3869
Biso mean--53.97 60.96 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093916
X-RAY DIFFRACTIONf_angle_d1.25354
X-RAY DIFFRACTIONf_chiral_restr0.063624
X-RAY DIFFRACTIONf_plane_restr0.01718
X-RAY DIFFRACTIONf_dihedral_angle_d12.2123114
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2250X-RAY DIFFRACTION10.217TORSIONAL
12B2250X-RAY DIFFRACTION10.217TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.26-2.31660.37011400.27762451100
2.3166-2.37920.33331450.26542421100
2.3792-2.44920.30181480.24342403100
2.4492-2.52820.25151410.22722416100
2.5282-2.61860.29731510.21022438100
2.6186-2.72340.23491340.2092448100
2.7234-2.84730.26351440.22062430100
2.8473-2.99740.29421450.22712441100
2.9974-3.18510.28691440.22622429100
3.1851-3.43090.26411440.21142437100
3.4309-3.77590.22721440.1861241899
3.7759-4.32170.17741420.1446241799
4.3217-5.44260.15151490.128242299
5.4426-39.540.15111400.138245098
Refinement TLS params.Method: refined / Origin x: 33.0996 Å / Origin y: 76.7989 Å / Origin z: 57.546 Å
111213212223313233
T0.4525 Å20.0983 Å2-0.0043 Å2-0.4052 Å2-0.0337 Å2--0.4452 Å2
L0.3549 °20.1619 °20.0974 °2--0.0342 °20.1293 °2--0.4783 °2
S0.0678 Å °0.0036 Å °0.0706 Å °-0.0175 Å °-0.027 Å °-0.0124 Å °-0.006 Å °0.006 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB26 - 309
2X-RAY DIFFRACTION1allA26 - 309
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 57

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