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- PDB-2isb: Crystal structure of Fumarase of FUM-1 (NP_069927.1) from Archaeo... -

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Basic information

Entry
Database: PDB / ID: 2isb
TitleCrystal structure of Fumarase of FUM-1 (NP_069927.1) from Archaeoglobus Fulgidus at 1.66 A resolution
ComponentsFumarase
KeywordsLYASE / NP_069927.1 / Fumarase of FUM-1 / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homologyfumarase / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain superfamily / Fumarase C-terminus / hydro-lyase activity / Alpha-Beta Barrel / Alpha Beta / Fumarase (Fum-1)
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Fumarase of FUM-1 (NP_069927.1) from Archaeoglobus Fulgidus at 1.66 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 17, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionNov 28, 2006ID: 1VPJ
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fumarase


Theoretical massNumber of molelcules
Total (without water)21,8831
Polymers21,8831
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.664, 51.664, 157.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Fumarase / Fum-1


Mass: 21882.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: FUM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O29167, fumarate hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.8
Details: 0.2M Li Acetate, 20.0% PEG-3350, No Buffer, pH 7.8, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00000, 0.97966, 0.97950
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979661
30.97951
ReflectionResolution: 1.66→21.152 Å / Num. obs: 25660 / % possible obs: 97.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.66-1.7540.66411268631340.66486.2
1.75-1.865.50.4341.51915035090.43499.1
1.86-1.986.80.2881.82281833530.28899.9
1.98-2.147.10.1873.42227631370.18799.9
2.14-2.357.10.134.12049729070.13100
2.35-2.6270.1026.31861226510.102100
2.62-3.036.90.0797.71640323650.079100
3.03-3.716.70.0619.31370920310.06199.9
3.71-5.256.50.0549.71059016210.05499.9
5.25-21.185.90.0547.856009520.05497.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.66→21.152 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.292 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.087
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3. DENSITY IS WEAK FOR THE FOLLOWING REGIONS: A-3 - 1, A70 - 73.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1256 4.9 %RANDOM
Rwork0.174 ---
obs0.175 25585 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.333 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.66→21.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 0 182 1581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221510
X-RAY DIFFRACTIONr_bond_other_d0.0010.021035
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9622069
X-RAY DIFFRACTIONr_angle_other_deg0.94132538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55423.03656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61115262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.826159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021709
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02312
X-RAY DIFFRACTIONr_nbd_refined0.2040.2258
X-RAY DIFFRACTIONr_nbd_other0.1970.21092
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2726
X-RAY DIFFRACTIONr_nbtor_other0.0880.2814
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1880.212
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.217
X-RAY DIFFRACTIONr_mcbond_it2.2263988
X-RAY DIFFRACTIONr_mcbond_other0.5053393
X-RAY DIFFRACTIONr_mcangle_it2.83551553
X-RAY DIFFRACTIONr_scbond_it4.9538608
X-RAY DIFFRACTIONr_scangle_it6.88911500
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 70 -
Rwork0.249 1447 -
obs-1517 80.65 %
Refinement TLS params.Method: refined / Origin x: 41.8297 Å / Origin y: 28.2611 Å / Origin z: 12.9866 Å
111213212223313233
T-0.0226 Å20.0142 Å2-0.0086 Å2--0.0657 Å2-0.0001 Å2---0.039 Å2
L0.8986 °20.0358 °20.3968 °2-0.7952 °2-0.0901 °2--1.4651 °2
S0.0216 Å °-0.0074 Å °-0.0807 Å °0.0546 Å °-0.0006 Å °-0.0205 Å °0.1782 Å °0.0415 Å °-0.021 Å °
Refinement TLS groupSelection: ALL

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