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- PDB-1v3w: Structure of Ferripyochelin binding protein from Pyrococcus horik... -

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Basic information

Entry
Database: PDB / ID: 1v3w
TitleStructure of Ferripyochelin binding protein from Pyrococcus horikoshii OT3
Componentsferripyochelin binding protein
KeywordsTRANSFERASE / BETA-HELIX / Carbonic anhydrase / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Dynactin subunit 5 / : / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
173aa long hypothetical ferripyochelin binding protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsJeyakanthan, J. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii.
Authors: Jeyakanthan, J. / Rangarajan, S. / Mridula, P. / Kanaujia, S.P. / Shiro, Y. / Kuramitsu, S. / Yokoyama, S. / Sekar, K.
History
DepositionNov 7, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 30, 2013Group: Structure summary
Revision 1.4Oct 25, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: ferripyochelin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,48411
Polymers18,9451
Non-polymers53910
Water3,477193
1
A: ferripyochelin binding protein
hetero molecules

A: ferripyochelin binding protein
hetero molecules

A: ferripyochelin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,45233
Polymers56,8343
Non-polymers1,61830
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation82_555-y,z,-x1
Buried area9360 Å2
ΔGint-134 kcal/mol
Surface area18300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)156.156, 156.156, 156.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-3002-

CA

21A-3004-

CA

31A-3005-

CA

41A-3174-

HOH

51A-3175-

HOH

61A-3187-

HOH

71A-3188-

HOH

81A-3189-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ferripyochelin binding protein


Mass: 18944.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus(DE3)-RIL / References: UniProt: O59257, carbonic anhydrase

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Non-polymers , 6 types, 203 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1.79 Å3/Da / Density % sol: 30.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, Hepes, CALCIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
20.02 MTris1droppH8.0
30.2 M1dropNaCl
426 %PEG40001reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Sep 28, 2003 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 26357 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 7.9 / Num. unique all: 26357 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 120843
Reflection shell
*PLUS
% possible obs: 99.8 % / Num. unique obs: 2602

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QQ0

1qq0


Resolution: 1.5→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2598 -RANDOM
Rwork0.185 ---
all-26665 --
obs-26248 98.4 %-
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1332 0 24 193 1549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.219 430 -
Rwork0.195 --
obs-3889 98.9 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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