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- PDB-2oqh: Crystal structure of an isomerase from Streptomyces coelicolor A3(2) -

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Basic information

Entry
Database: PDB / ID: 2oqh
TitleCrystal structure of an isomerase from Streptomyces coelicolor A3(2)
ComponentsPutative isomerase
KeywordsISOMERASE / 9291a / PSI-II / PSI-2 / NYSGXRC / enolase / tim barrel / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


glucarate dehydratase / isomerase activity / metal ion binding
Similarity search - Function
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 ...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
glucarate dehydratase
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an isomerase from Streptomyces coelicolor
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ... BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS A MONOMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative isomerase
B: Putative isomerase
C: Putative isomerase
D: Putative isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,3598
Polymers166,9754
Non-polymers3844
Water17,024945
1
A: Putative isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8402
Polymers41,7441
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8402
Polymers41,7441
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8402
Polymers41,7441
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8402
Polymers41,7441
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Putative isomerase
C: Putative isomerase
hetero molecules

A: Putative isomerase
C: Putative isomerase
hetero molecules

A: Putative isomerase
C: Putative isomerase
hetero molecules

A: Putative isomerase
C: Putative isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,71816
Polymers333,9508
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area27680 Å2
ΔGint-182 kcal/mol
Surface area93070 Å2
MethodPISA, PQS
6
B: Putative isomerase
D: Putative isomerase
hetero molecules

B: Putative isomerase
D: Putative isomerase
hetero molecules

B: Putative isomerase
D: Putative isomerase
hetero molecules

B: Putative isomerase
D: Putative isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,71816
Polymers333,9508
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)120.336, 120.336, 126.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
Putative isomerase


Mass: 41743.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Species: Streptomyces coelicolor / Strain: A3(2), M145 / Gene: SCO7570, SC5F1.24 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus RIL / References: UniProt: Q9F3A5
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 945 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, pH 6.5, 12% PEG 20000, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 26, 2007 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 125276 / Num. obs: 125276 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.6
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1 / Num. unique all: 12509 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→36.45 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 104391.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3682 3 %RANDOM
Rwork0.205 ---
all0.205 121653 --
obs0.205 121653 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4667 Å2 / ksol: 0.377628 e/Å3
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.98→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11024 0 20 945 11989
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 1.98→2.1 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 607 3.2 %
Rwork0.228 18649 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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