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- PDB-1su0: Crystal structure of a hypothetical protein at 2.3 A resolution -

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Basic information

Entry
Database: PDB / ID: 1su0
TitleCrystal structure of a hypothetical protein at 2.3 A resolution
ComponentsNifU like protein IscU
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NifU / IscU / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


iron-sulfur cluster assembly / iron-sulfur cluster binding / iron ion binding
Similarity search - Function
Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Iron-sulfur cluster assembly scaffold protein IscU
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLiu, J. / Oganesyan, N. / Shin, D.-H. / Jancarik, J. / Pufan, R. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2005
Title: Structural characterization of an iron-sulfur cluster assembly protein IscU in a zinc-bound form.
Authors: Liu, J. / Oganesyan, N. / Shin, D.H. / Jancarik, J. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionMar 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: NifU like protein IscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2302
Polymers17,1641
Non-polymers651
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.014, 72.014, 112.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein NifU like protein IscU


Mass: 17164.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A1G2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.9 M Sodium Malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794, 0.9796, 0.9600
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2003
RadiationMonochromator: YALE MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.961
ReflectionResolution: 2.3→60 Å / Num. all: 7056 / Num. obs: 6915 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.359 Å / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.845 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25582 320 4.7 %RANDOM
Rwork0.21981 ---
obs0.2215 6457 98.27 %-
all-6570 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.217 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 1 22 1049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211042
X-RAY DIFFRACTIONr_bond_other_d0.0020.02941
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9531406
X-RAY DIFFRACTIONr_angle_other_deg0.84832207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6895135
X-RAY DIFFRACTIONr_chiral_restr0.0830.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021168
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02182
X-RAY DIFFRACTIONr_nbd_refined0.2360.2291
X-RAY DIFFRACTIONr_nbd_other0.2310.21180
X-RAY DIFFRACTIONr_nbtor_other0.0930.2623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.290.243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.244
X-RAY DIFFRACTIONr_mcbond_it0.5521.5675
X-RAY DIFFRACTIONr_mcangle_it1.01821077
X-RAY DIFFRACTIONr_scbond_it1.5633367
X-RAY DIFFRACTIONr_scangle_it2.364.5329
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.385 11
Rwork0.372 399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
128.96710.61079.981814.4788-4.061921.71940.20310.92681.10320.2503-0.2537-1.42680.02631.02860.05060.11630.120.15030.12740.14870.583130.510229.435715.0012
211.08720.4437-0.376212.191-3.60513.5315-0.33381.1835-0.2446-0.78620.53170.72111.5469-1.8435-0.19790.5201-0.26480.03130.93550.25810.205211.723527.66875.3023
39.61744.8607-6.00387.1506-5.173414.20840.15590.73740.8380.12280.41070.59440.1209-0.9301-0.56660.0917-0.01330.05570.3570.2310.255613.932831.283218.1416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BA7 - 207 - 20
2X-RAY DIFFRACTION2BA21 - 6421 - 64
3X-RAY DIFFRACTION3BA65 - 14165 - 141

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