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- PDB-3dip: Crystal structure of an enolase protein from the environmental ge... -

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Basic information

Entry
Database: PDB / ID: 3dip
TitleCrystal structure of an enolase protein from the environmental genome shotgun sequencing of the Sargasso Sea
Componentsenolase
KeywordsLYASE / STRUCTURAL GENOMICS / ISOMERASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyEnolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Zhang, F. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an enolase protein from the environmental genome shotgun sequencing of the Sargasso Sea
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Zhang, F. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJun 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / struct_ref_seq
Item: _audit_author.identifier_ORCID / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_main_chain_plane.improper_torsion_angle

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: enolase
B: enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7396
Polymers88,3552
Non-polymers3844
Water4,161231
1
A: enolase
B: enolase
hetero molecules

A: enolase
B: enolase
hetero molecules

A: enolase
B: enolase
hetero molecules

A: enolase
B: enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,95624
Polymers353,4198
Non-polymers1,53716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area33030 Å2
ΔGint-42 kcal/mol
Surface area84330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)282.292, 282.292, 282.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432

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Components

#1: Protein enolase /


Mass: 44177.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8
Details: 100mM Tris HCl pH 8.0, 1.5M ammonium sulfate, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97958 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.5→47.727 Å / Num. all: 33847 / Num. obs: 33847 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 42.2 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 30.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 43.1 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 12.9 / Num. measured all: 208049 / Num. unique all: 4831 / Rsym value: 0.295 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.751 / SU B: 8.44 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.445 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ASP321 OBSERVED TO HAVE CYCLIZED WITH AMIDE OF CYS322 - TOGETHER THESE AMINO ACIDS MODELED AS HET GROUP SIC
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1728 5.1 %RANDOM
Rwork0.215 ---
obs0.218 33753 100 %-
all-33753 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 83.69 Å2 / Biso mean: 30.413 Å2 / Biso min: 6.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 20 231 5817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225706
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9687774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73522.358229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98215870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8951553
X-RAY DIFFRACTIONr_chiral_restr0.0880.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024319
X-RAY DIFFRACTIONr_nbd_refined0.2050.22665
X-RAY DIFFRACTIONr_nbtor_refined0.30.23907
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2333
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.222
X-RAY DIFFRACTIONr_mcbond_it0.6571.53770
X-RAY DIFFRACTIONr_mcangle_it1.09325852
X-RAY DIFFRACTIONr_scbond_it1.76332188
X-RAY DIFFRACTIONr_scangle_it2.8394.51922
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.525 140 -
Rwork0.356 2274 -
all-2414 -
obs-2274 100 %

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