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- PDB-2ovl: Crystal structure of a racemase from Streptomyces coelicolor A3(2) -

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Basic information

Entry
Database: PDB / ID: 2ovl
TitleCrystal structure of a racemase from Streptomyces coelicolor A3(2)
ComponentsPutative racemaseEpimerase and racemase
KeywordsISOMERASE / racemase / Streptomyces coelicolor A3(2) / 9301a / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


3,6-anhydro-L-galactonate cycloisomerase / galactose catabolic process / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / isomerase activity / magnesium ion binding
Similarity search - Function
3,6-anhydro-alpha-L-galactonate cycloisomerase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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 ...3,6-anhydro-alpha-L-galactonate cycloisomerase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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
3,6-anhydro-alpha-L-galactonate cycloisomerase
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsRao, K.N. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a racemase from Streptomyces coelicolor A3(2)
Authors: Rao, K.N. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / 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 / _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_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.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)164,9238
Polymers164,8314
Non-polymers924
Water7,152397
1
A: Putative racemase
B: Putative racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4624
Polymers82,4162
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-27 kcal/mol
Surface area26130 Å2
MethodPISA
2
C: Putative racemase
D: Putative racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4624
Polymers82,4162
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-39 kcal/mol
Surface area26060 Å2
MethodPISA
3
A: Putative racemase
B: Putative racemase
hetero molecules

A: Putative racemase
B: Putative racemase
hetero molecules

A: Putative racemase
B: Putative racemase
hetero molecules

A: Putative racemase
B: Putative racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,84716
Polymers329,6638
Non-polymers1848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area32470 Å2
ΔGint-124 kcal/mol
Surface area87060 Å2
MethodPISA
4
C: Putative racemase
D: Putative racemase
hetero molecules

C: Putative racemase
D: Putative racemase
hetero molecules

C: Putative racemase
D: Putative racemase
hetero molecules

C: Putative racemase
D: Putative racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,84716
Polymers329,6638
Non-polymers1848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area32820 Å2
ΔGint-169 kcal/mol
Surface area86840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.603, 177.603, 111.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
Putative racemase / Epimerase and racemase


Mass: 41207.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Species: Streptomyces coelicolorStreptomyces albidoflavus / Strain: A3(2), M145 / Gene: SCO3480, SCE65.16c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RKF7
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3M Sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2007 / Details: Mirrors
RadiationMonochromator: Silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. all: 100173 / Num. obs: 100173 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.6 % / Biso Wilson estimate: 22.4 Å2 / Rsym value: 0.063 / Net I/σ(I): 12.1
Reflection shellResolution: 2.13→2.21 Å / Redundancy: 27.8 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 2.5 / Num. unique all: 9789 / Rsym value: 0.228 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: none

Resolution: 2.13→32.05 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 98201.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2431 2.5 %RANDOM
Rwork0.215 ---
all0.215 97191 --
obs0.215 97191 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.5636 Å2 / ksol: 0.385628 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å20 Å2
2--2.78 Å20 Å2
3----5.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.13→32.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10824 0 4 397 11225
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 2.13→2.26 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 383 2.5 %
Rwork0.23 15150 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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