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- PDB-2nql: Crystal structure of a member of the enolase superfamily from Agr... -

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Basic information

Entry
Database: PDB / ID: 2nql
TitleCrystal structure of a member of the enolase superfamily from Agrobacterium tumefaciens
ComponentsIsomerase/lactonizing enzyme
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ENOLASE / PROTEIN STRUCTURE INITIATIVE / PSI / NYSGXRC / New York SGX Research Center for Structural Genomics STRUCTURAL GENOMICS
Function / homology
Function and homology information


amino acid catabolic process / isomerase activity / magnesium ion binding
Similarity search - Function
Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain ...Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Isomerase/lactonizing enzyme / :
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPatskovsky, Y. / Ramagopal, U. / Toro, R. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Gerlt, J. / Burley, S.K. ...Patskovsky, Y. / Ramagopal, U. / Toro, R. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Gerlt, J. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Enolase from Agrobacterium Tumefaciens C58
Authors: Patskovsky, Y. / Ramagopal, U. / Toro, R. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Gerlt, J. / Burley, S.K. / Almo, S.C.
History
DepositionOct 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 600 HETEROGEN The authors state that a density in the map which corresponds to a ligand that resembles ... HETEROGEN The authors state that a density in the map which corresponds to a ligand that resembles benzoic acid was observed. The model of benzoic acid represents one of the possible ligands which can be fitted in that density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isomerase/lactonizing enzyme
B: Isomerase/lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,37323
Polymers84,7182
Non-polymers1,65521
Water16,123895
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-187 kcal/mol
Surface area27790 Å2
MethodPISA
2
B: Isomerase/lactonizing enzyme
hetero molecules

B: Isomerase/lactonizing enzyme
hetero molecules

A: Isomerase/lactonizing enzyme
hetero molecules

A: Isomerase/lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,74746
Polymers169,4364
Non-polymers3,31042
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
crystal symmetry operation6_654x-y+1,x,z-1/61
crystal symmetry operation8_665x-y+1,-y+1,-z1
Buried area19800 Å2
ΔGint-369 kcal/mol
Surface area53480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.071, 102.071, 369.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-1671-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 1 - 388 / Label seq-ID: 1 - 388

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Isomerase/lactonizing enzyme / AGR_pAT_674p


Mass: 42359.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: AGR_pAT_674 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UJL8, UniProt: A9CL63*PLUS

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Non-polymers , 5 types, 916 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 895 / 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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100MM SODIUM CACODYLATE, PH 6.5, 2M AMMONIUM SULFATE, 100MM NACL, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 106184 / Num. obs: 106184 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.068 / Rsym value: 0.064 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10308 / Rsym value: 0.41 / % possible all: 99

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GL5

2gl5


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.185 / SU ML: 0.068 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -5 / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20144 3183 -RANDOM
Rwork0.16937 ---
all0.17036 102915 --
obs0.17036 102915 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.165 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5968 0 111 895 6974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226337
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9718643
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87623.217286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.573151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1741556
X-RAY DIFFRACTIONr_chiral_restr0.1960.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024894
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.33220
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.54319
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.51325
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2560.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.383
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.576
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.31923917
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.24736297
X-RAY DIFFRACTIONr_scbond_it5.86132520
X-RAY DIFFRACTIONr_scangle_it8.43252325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2882 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.640.5
medium thermal1.722
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 229 -
Rwork0.255 7245 -
obs-7474 97.61 %

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