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- PDB-6ive: Molecular structure of a thermostable and a Zinc ion binding gamm... -

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Basic information

Entry
Database: PDB / ID: 6ive
TitleMolecular structure of a thermostable and a Zinc ion binding gamma-class carbonic anhydrase
ComponentsFerripyochelin-binding protein
KeywordsMETAL BINDING PROTEIN / Gamma-class carbonic anhydrase Metal binding protein
Function / homology
Function and homology information


: / : / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ferripyochelin-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, W.M. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21601112, 21671125 China
CitationJournal: Biometals / Year: 2019
Title: Molecular structure of thermostable and zinc-ion-binding gamma-class carbonic anhydrases.
Authors: Wang, W. / Zhang, Y. / Wang, L. / Jing, Q. / Wang, X. / Xi, X. / Zhao, X. / Wang, H.
History
DepositionDec 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _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.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.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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferripyochelin-binding protein
B: Ferripyochelin-binding protein
C: Ferripyochelin-binding protein
D: Ferripyochelin-binding protein
E: Ferripyochelin-binding protein
F: Ferripyochelin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,82518
Polymers104,8636
Non-polymers96212
Water7,062392
1
A: Ferripyochelin-binding protein
B: Ferripyochelin-binding protein
C: Ferripyochelin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9139
Polymers52,4313
Non-polymers4816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-181 kcal/mol
Surface area16630 Å2
MethodPISA
2
D: Ferripyochelin-binding protein
E: Ferripyochelin-binding protein
F: Ferripyochelin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9139
Polymers52,4313
Non-polymers4816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-181 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.687, 69.232, 83.334
Angle α, β, γ (deg.)75.22, 74.39, 89.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ferripyochelin-binding protein


Mass: 17477.125 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1879 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SH51
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 200mM tripotassium orthophosphate (pH 8.9), 19% (wt/vol) PEG 3350, 5% (vol/vol) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 44102 / % possible obs: 97.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.196 / Rrim(I) all: 0.196 / Χ2: 0.665 / Net I/av σ(I): 7.83 / Net I/σ(I): 7.83
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2 / CC1/2: 0.848 / Χ2: 0.522 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N27

4n27


Resolution: 2.3→46.809 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.28
RfactorNum. reflection% reflection
Rfree0.223 2001 4.55 %
Rwork0.1811 --
obs0.183 44018 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7250 0 36 392 7678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037454
X-RAY DIFFRACTIONf_angle_d0.64310206
X-RAY DIFFRACTIONf_dihedral_angle_d12.5024372
X-RAY DIFFRACTIONf_chiral_restr0.0541155
X-RAY DIFFRACTIONf_plane_restr0.0051369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2878-2.34510.27211370.22842671X-RAY DIFFRACTION87
2.3451-2.40850.30031290.21653028X-RAY DIFFRACTION96
2.4085-2.47930.23411470.21022985X-RAY DIFFRACTION96
2.4793-2.55930.25871480.21223042X-RAY DIFFRACTION97
2.5593-2.65080.27691380.21362969X-RAY DIFFRACTION97
2.6508-2.75690.24091510.20433032X-RAY DIFFRACTION96
2.7569-2.88240.241400.20993038X-RAY DIFFRACTION97
2.8824-3.03430.23691510.19463021X-RAY DIFFRACTION97
3.0343-3.22440.24841420.2053010X-RAY DIFFRACTION97
3.2244-3.47330.28231430.18793083X-RAY DIFFRACTION98
3.4733-3.82270.21721460.16953039X-RAY DIFFRACTION98
3.8227-4.37550.17911430.14513051X-RAY DIFFRACTION98
4.3755-5.51120.15191400.14133023X-RAY DIFFRACTION97
5.5112-46.81930.18591460.16033025X-RAY DIFFRACTION97

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