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- PDB-1gvc: 18kDa N-II domain fragment of duck ovotransferrin + NTA -

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Basic information

Entry
Database: PDB / ID: 1gvc
Title18kDa N-II domain fragment of duck ovotransferrin + NTA
ComponentsOVOTRANSFERRIN
KeywordsIRON TRANSPORT / GLYCOPROTEIN / METAL-BINDING
Function / homology
Function and homology information


iron ion transport / extracellular space / metal ion binding
Similarity search - Function
Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II ...Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / NITRILOTRIACETIC ACID / Ovotransferrin
Similarity search - Component
Biological speciesANAS PLATYRHYNCHOS (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsKuser, P. / Hall, D.R. / Haw, M.L. / Neu, M. / Lindley, P.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The Mechanism of Iron Uptake by Transferrins: The X-Ray Structures of the 18 kDa Nii Domain Fragment of Duck Ovotransferrin and its Nitrilotriacetate Complex
Authors: Kuser, P. / Hall, D.R. / Haw, M.L. / Neu, M. / Evans, R. / Lindley, P.F.
History
DepositionFeb 7, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OVOTRANSFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5234
Polymers17,2161
Non-polymers3073
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.410, 41.410, 81.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein OVOTRANSFERRIN /


Mass: 17216.471 Da / Num. of mol.: 1 / Fragment: N-II FRAGMENT, RESIDUES 91-247 / Source method: isolated from a natural source / Details: COMPLEX OF DUCK OVOTRANSFERRIN FRAGMENT AND NTA / Source: (natural) ANAS PLATYRHYNCHOS (mallard) / References: UniProt: P56410
#2: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-NTA / NITRILOTRIACETIC ACID / Nitrilotriacetic acid


Mass: 191.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO6
#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCED BY DR. R.W.EVANS (GUY'S HOSPITAL) LONDON, U.K. THESE AMINO-ACID RESIDUES DIFFER FROM ...SEQUENCED BY DR. R.W.EVANS (GUY'S HOSPITAL) LONDON, U.K. THESE AMINO-ACID RESIDUES DIFFER FROM THOSE GIVEN BY SWISS-PROT.

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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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: SITTING DROP AT PH7.8 AND 277K, pH 7.80
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMTris-HCl1drop
220-40 mg/mlprotein1drop
323 %methanepentanediol1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.88
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 15, 1993 / Details: PT COATED FUSED QUARTZ
RadiationMonochromator: TRIANGULAR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.9→26.92 Å / Num. obs: 12081 / % possible obs: 98 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 7.6 / % possible all: 97.3
Reflection
*PLUS
Num. measured all: 52160
Reflection shell
*PLUS
% possible obs: 97.3 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
Agrovatadata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.9→26.92 Å / SU B: 4.873 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R Free: 0.139 / Details: RESIDUES E144 - S148 INCLUSIVE ARE POORLY DEFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.211 573 4.8 %RANDOM
Rwork0.185 ---
obs0.186 11481 98.05 %-
Refinement stepCycle: LAST / Resolution: 1.9→26.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 18 96 1318
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.68
X-RAY DIFFRACTIONp_plane_restr0.006

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