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- PDB-3v77: Crystal structure of a putative fumarylacetoacetate isomerase/hyd... -

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Basic information

Entry
Database: PDB / ID: 3v77
TitleCrystal structure of a putative fumarylacetoacetate isomerase/hydrolase from Oleispira antarctica
ComponentsPutative fumarylacetoacetate isomerase/hydrolase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / OCEAN METAGENOMICS
Function / homology
Function and homology information


Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / D(-)-TARTARIC ACID / Putative fumarylacetoacetate isomerase/hydrolase
Similarity search - Component
Biological speciesOleispira antarctica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStogios, P.J. / Kagan, O. / Di Leo, R. / Bochkarev, A. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Nat Commun / Year: 2013
Title: Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.
Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / ...Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / Lunsdorf, H. / Fernandez, M. / Juarez, S. / Ciordia, S. / Singer, A. / Kagan, O. / Egorova, O. / Alain Petit, P. / Stogios, P. / Kim, Y. / Tchigvintsev, A. / Flick, R. / Denaro, R. / Genovese, M. / Albar, J.P. / Reva, O.N. / Martinez-Gomariz, M. / Tran, H. / Ferrer, M. / Savchenko, A. / Yakunin, A.F. / Yakimov, M.M. / Golyshina, O.V. / Reinhardt, R. / Golyshin, P.N.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionJan 18, 2012ID: 3L53
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative fumarylacetoacetate isomerase/hydrolase
B: Putative fumarylacetoacetate isomerase/hydrolase
C: Putative fumarylacetoacetate isomerase/hydrolase
D: Putative fumarylacetoacetate isomerase/hydrolase
E: Putative fumarylacetoacetate isomerase/hydrolase
F: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,01528
Polymers144,8526
Non-polymers2,16322
Water21,1681175
1
A: Putative fumarylacetoacetate isomerase/hydrolase
D: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,19911
Polymers48,2842
Non-polymers9159
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-117 kcal/mol
Surface area17590 Å2
MethodPISA
2
B: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules

E: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8338
Polymers48,2842
Non-polymers5496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3810 Å2
ΔGint-84 kcal/mol
Surface area17420 Å2
MethodPISA
3
C: Putative fumarylacetoacetate isomerase/hydrolase
F: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9839
Polymers48,2842
Non-polymers6997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-85 kcal/mol
Surface area17220 Å2
MethodPISA
4
A: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6326
Polymers24,1421
Non-polymers4905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4174
Polymers24,1421
Non-polymers2753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
C: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5675
Polymers24,1421
Non-polymers4254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
D: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5675
Polymers24,1421
Non-polymers4254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
E: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4174
Polymers24,1421
Non-polymers2753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
F: Putative fumarylacetoacetate isomerase/hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4174
Polymers24,1421
Non-polymers2753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.265, 161.386, 114.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
Putative fumarylacetoacetate isomerase/hydrolase


Mass: 24142.076 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oleispira antarctica (bacteria) / Plasmid: P15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D2YW46
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1175 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.2 M DI-AMMONIUM TARTRATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 10 MM ZINC SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 99078 / Num. obs: 97790 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.061 / Net I/σ(I): 20.88
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.76 / Rsym value: 0.253 / % possible all: 83.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GTT

1gtt


Resolution: 2.1→27.51 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.806 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25592 4262 5 %RANDOM
Rwork0.19867 ---
obs0.20156 81063 99.64 %-
all-81356 --
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: 35.105 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10128 0 121 1175 11424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210459
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.99314226
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17251346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39925.673416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.561151734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7381536
X-RAY DIFFRACTIONr_chiral_restr0.090.21648
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0227908
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6391.56732
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.182210836
X-RAY DIFFRACTIONr_scbond_it1.66833727
X-RAY DIFFRACTIONr_scangle_it2.7874.53386
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 308 -
Rwork0.237 5782 -
obs--97.71 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
132.4652-43.6252-5.9998
229.7295-43.2816-6.321
333.2793-38.2175-10.1471
442.659-15.94621.7256
541.2931-15.319219.4757
643.421-21.593818.6099
7-7.3648-20.8508-6.9745
8-5.4197-20.9881-4.926
9-3.5556-18.7276-11.5381
1015.3935-60.11145.5873
1117.3235-58.90736.3871
1213.1011-63.2059.9511
1333.6162-8.1158-22.8762
1435.8297-7.6541-21.5827
1534.1098-14.6493-22.0348
16-12.9562-28.303417.6901
17-12.1991-30.148315.4973
18-13.5827-33.282121.6012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 37
2X-RAY DIFFRACTION2A38 - 150
3X-RAY DIFFRACTION3A151 - 224
4X-RAY DIFFRACTION4B1 - 37
5X-RAY DIFFRACTION5B38 - 150
6X-RAY DIFFRACTION6B151 - 224
7X-RAY DIFFRACTION7C1 - 37
8X-RAY DIFFRACTION8C38 - 150
9X-RAY DIFFRACTION9C151 - 224
10X-RAY DIFFRACTION10D1 - 37
11X-RAY DIFFRACTION11D38 - 150
12X-RAY DIFFRACTION12D151 - 224
13X-RAY DIFFRACTION13E1 - 37
14X-RAY DIFFRACTION14E38 - 150
15X-RAY DIFFRACTION15E151 - 224
16X-RAY DIFFRACTION16F1 - 37
17X-RAY DIFFRACTION17F38 - 150
18X-RAY DIFFRACTION18F151 - 224

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