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- PDB-2gpj: CRYSTAL STRUCTURE OF A SIDEROPHORE-INTERACTING PROTEIN (SPUTCN32_... -

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Basic information

Entry
Database: PDB / ID: 2gpj
TitleCRYSTAL STRUCTURE OF A SIDEROPHORE-INTERACTING PROTEIN (SPUTCN32_0076) FROM SHEWANELLA PUTREFACIENS CN-32 AT 2.20 A RESOLUTION
ComponentsSiderophore-interacting protein
KeywordsFAD-BINDING PROTEIN / SIDEROPHORE-INTERACTING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Siderophore-interacting protein / Siderophore-interacting protein, C-terminal domain / FAD-binding 9, siderophore-interacting / Siderophore-interacting protein / Siderophore-interacting FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain ...Siderophore-interacting protein / Siderophore-interacting protein, C-terminal domain / FAD-binding 9, siderophore-interacting / Siderophore-interacting protein / Siderophore-interacting FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : / Siderophore-interacting protein
Similarity search - Component
Biological speciesShewanella putrefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of siderophore-interacting protein (ZP_00813641.1) from Shewanella putrefaciens CN-32 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Siderophore-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,13419
Polymers28,3761
Non-polymers1,75818
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.540, 100.540, 67.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Siderophore-interacting protein


Mass: 28376.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens (bacteria) / Strain: CN-32 / Gene: ZP_00813641.1 / Production host: Escherichia coli (E. coli) / References: GenBank: 77814381, UniProt: A4Y1H9*PLUS

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Non-polymers , 6 types, 113 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.84 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.6
Details: 0.02M CaCl2, 30.0% MPD, 0.1M Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97917
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2006 / Details: Flat mirror (vertical focusing)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.2→28.76 Å / Num. obs: 18135 / % possible obs: 96.8 % / Biso Wilson estimate: 43.254 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.280.763212638306589.3
2.28-2.370.6692.313194309393.8
2.37-2.480.5972.613950325995
2.48-2.610.4783.313703319596.4
2.61-2.770.3744.113796322297.8
2.77-2.980.2655.614000326298.2
2.98-3.280.1648.414335335099.1
3.28-3.760.09912.214372338299.4
3.760.06617.413942332599.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→28.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.732 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.183
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). ACETATE, CHLORIDE, AND CALCIUM IONS FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. 3). AN ACETATE AND A CA ION ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). ACETATE, CHLORIDE, AND CALCIUM IONS FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. 3). AN ACETATE AND A CA ION WERE TENTATIVELY MODELED INTO DENSITY NEAR HIS 213. 4). SEVERAL MOLECULES OF ETHYLENE GLYCOL, USED AS A CRYOPROTECTANT, WERE MODELED INTO THE STRUCTURE. 5). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL SE-MET INCORPORATION. 6). A FLAVIN ADENINE DINUCLEOTIDE MOLECULE WAS OBSERVED IN THE ACTIVE SITE OF THE PROTEIN. 7). UNEXPLAININED ELECTRON DENSITIES ALONG CRYSTALLOGRAPHIC SYMMETRY AXES WERE NOT MODELED. 8). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 923 5.1 %RANDOM
Rwork0.176 ---
obs0.179 18093 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 112 95 2117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222091
X-RAY DIFFRACTIONr_bond_other_d0.0010.021885
X-RAY DIFFRACTIONr_angle_refined_deg1.2332.0022838
X-RAY DIFFRACTIONr_angle_other_deg0.62434381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65724.45792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20415318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3431511
X-RAY DIFFRACTIONr_chiral_restr0.0680.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
X-RAY DIFFRACTIONr_nbd_refined0.2210.2395
X-RAY DIFFRACTIONr_nbd_other0.2170.21847
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2937
X-RAY DIFFRACTIONr_nbtor_other0.0920.21123
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.292
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.26
X-RAY DIFFRACTIONr_mcbond_it3.0431291
X-RAY DIFFRACTIONr_mcbond_other0.8133494
X-RAY DIFFRACTIONr_mcangle_it4.16352006
X-RAY DIFFRACTIONr_scbond_it7.2898956
X-RAY DIFFRACTIONr_scangle_it8.87311832
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 83 -
Rwork0.293 1229 -
obs-1312 99.85 %
Refinement TLS params.Method: refined / Origin x: 0.815 Å / Origin y: 27.82 Å / Origin z: 4.719 Å
111213212223313233
T-0.2144 Å2-0.0036 Å2-0.0268 Å2--0.1902 Å20.0153 Å2---0.0154 Å2
L1.6482 °2-0.0627 °2-0.0968 °2-1.6529 °20.1237 °2--2.0833 °2
S0.0502 Å °-0.1897 Å °-0.0615 Å °0.0327 Å °-0.0804 Å °0.1868 Å °-0.0171 Å °-0.0385 Å °0.0303 Å °
Refinement TLS groupSelection: ALL

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