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- PDB-3ck5: Crystal structure of a racemase from Streptomyces coelicolor A3(2... -

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Basic information

Entry
Database: PDB / ID: 3ck5
TitleCrystal structure of a racemase from Streptomyces coelicolor A3(2) with bound magnesium
ComponentsPutative racemase
KeywordsISOMERASE / RACEMASE / Magnesium / 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 / FOURIER SYNTHESIS / Resolution: 2.3 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) with bound magnesium.
Authors: Rao, K.N. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 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 racemase
B: Putative racemase
C: Putative racemase
D: Putative racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,9298
Polymers164,8314
Non-polymers974
Water6,053336
1
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)329,85716
Polymers329,6638
Non-polymers1948
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 area32150 Å2
ΔGint-83 kcal/mol
Surface area86480 Å2
MethodPISA
2
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)329,85716
Polymers329,6638
Non-polymers1948
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 area32850 Å2
ΔGint-45.5 kcal/mol
Surface area86080 Å2
MethodPISA
3
A: Putative racemase
B: Putative racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4644
Polymers82,4162
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-13.6 kcal/mol
Surface area26040 Å2
MethodPISA
4
C: Putative racemase
D: Putative racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4644
Polymers82,4162
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-13.8 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.603, 177.603, 112.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11C-472-

HOH

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Components

#1: Protein
Putative 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 coelicolor / Strain: A3(2), M145 / Gene: SCO3480, SCE65.16c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RKF7
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Na acetate, 0.2M Mg chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 79289 / Num. obs: 79289 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.2 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.35 / Num. unique all: 7816 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2OVL

2ovl


Resolution: 2.3→49.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 48734.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1876 2.5 %RANDOM
Rwork0.224 ---
obs0.224 75376 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.3427 Å2 / ksol: 0.348715 e/Å3
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.92 Å20 Å20 Å2
2--3.92 Å20 Å2
3----7.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10824 0 4 336 11164
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.442.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 313 2.7 %
Rwork0.276 11217 -
obs--87.9 %
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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