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- PDB-2vp1: Fe-FutA2 from Synechocystis PCC6803 -

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Basic information

Entry
Database: PDB / ID: 2vp1
TitleFe-FutA2 from Synechocystis PCC6803
ComponentsPERIPLASMIC IRON-BINDING PROTEIN
KeywordsMETAL BINDING PROTEIN / FERRIC BINDING PROTEIN / METAL-BINDING PROTEIN / TAT / IRON / FUTA2 / SYNECHOCYSTIS
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / iron ion transport / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Ferric binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Iron uptake protein A2
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBadarau, A. / Firbank, S.J. / Banfield, M.J. / Dennison, C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Futa2 is a Ferric Binding Protein from Synechocystis Pcc 6803.
Authors: Badarau, A. / Firbank, S.J. / Waldron, K.J. / Yanagisawa, S. / Robinson, N.J. / Banfield, M.J. / Dennison, C.
History
DepositionFeb 26, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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_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

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Assembly

Deposited unit
A: PERIPLASMIC IRON-BINDING PROTEIN
B: PERIPLASMIC IRON-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9648
Polymers76,3912
Non-polymers5736
Water39622
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A: PERIPLASMIC IRON-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4824
Polymers38,1961
Non-polymers2873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PERIPLASMIC IRON-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4824
Polymers38,1961
Non-polymers2873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.340, 51.600, 100.740
Angle α, β, γ (deg.)90.00, 98.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PERIPLASMIC IRON-BINDING PROTEIN / FUTA2


Mass: 38195.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC 6803 / References: UniProt: Q55835
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6.5
Details: 27% PEG 4000, 0.2M MAGNESIUM CHLORIDE, 0.1M 2-(N-MORPHOLINO)ETHANESULPHONIC ACID (MES) PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→64.4 Å / Num. obs: 20641 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VOZ

2voz


Resolution: 2.7→30.21 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.832 / SU B: 12.485 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1059 5.1 %RANDOM
Rwork0.215 ---
obs0.218 19539 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.11 Å2
2--0.07 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 28 22 4926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225020
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9556840
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5055628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.21423.828256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19615763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1361545
X-RAY DIFFRACTIONr_chiral_restr0.0730.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023979
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22354
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23409
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.451.53192
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80525000
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1632083
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9564.51838
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: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.365 73
Rwork0.256 1476

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