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- PDB-3c3k: Crystal structure of an uncharacterized protein from Actinobacill... -

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Basic information

Entry
Database: PDB / ID: 3c3k
TitleCrystal structure of an uncharacterized protein from Actinobacillus succinogenes
ComponentsAlanine racemase
KeywordsISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / DNA-binding / Transcription / Transcription regulation / PSI-2
Function / homology
Function and homology information


alanine racemase / alanine racemase activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesActinobacillus succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.99 Å
AuthorsMalashkevich, V.N. / Toro, R. / Meyer, A.J. / 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 uncharacterized protein from Actinobacillus succinogenes.
Authors: Malashkevich, V.N. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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 / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine racemase
B: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5755
Polymers62,3562
Non-polymers2203
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.888, 67.602, 204.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alanine racemase /


Mass: 31177.781 Da / Num. of mol.: 2 / Fragment: Residues 54-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus succinogenes (bacteria) / Strain: 130Z / Gene: Asuc_0357 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A6VL88, alanine racemase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 1.94 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Magnesium chloride, 0.1 M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 3 % / Av σ(I) over netI: 8.4 / Number: 165629 / Rmerge(I) obs: 0.088 / Χ2: 1.28 / D res high: 1.99 Å / D res low: 50 Å / Num. obs: 55962 / % possible obs: 86.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.295099.710.0481.8413.6
3.44.2999.710.0682.1893.4
2.973.499.710.0861.373.3
2.72.9799.910.121.0633.3
2.512.799.610.1650.8863.2
2.362.5198.310.1940.8512.9
2.242.3692.810.220.8072.6
2.142.2478.510.2320.7612.2
2.062.1457.510.2410.7922
1.992.0638.410.2450.8061.8
ReflectionResolution: 1.99→50 Å / Num. obs: 55962 / % possible obs: 86.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.088 / Χ2: 1.283 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.99-2.061.80.24525170.806138.4
2.06-2.1420.24136600.792157.5
2.14-2.242.20.23250970.761178.5
2.24-2.362.60.2260130.807192.8
2.36-2.512.90.19464100.851198.3
2.51-2.73.20.16564500.886199.6
2.7-2.973.30.1264131.063199.9
2.97-3.43.30.08664551.37199.7
3.4-4.293.40.06864802.189199.7
4.29-503.60.04864671.841199.7

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Phasing

PhasingMethod: MAD
Phasing dmFOM : 0.64 / FOM acentric: 0.64 / FOM centric: 0.64 / Reflection: 31321 / Reflection acentric: 27080 / Reflection centric: 4241
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-31.0660.90.930.8416231100523
3.6-5.70.90.920.8246993836863
2.8-3.60.80.820.7157674959808
2.5-2.80.630.640.5757555072683
2.1-2.50.480.480.4696878707980
2-2.10.360.350.437903406384

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→30.47 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.527 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1596 5.1 %RANDOM
Rwork0.18 ---
obs0.183 31315 100 %-
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 mean: 19.901 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.99→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 13 253 4386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224197
X-RAY DIFFRACTIONr_angle_refined_deg1.9941.9745690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78524.94166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44615736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9731518
X-RAY DIFFRACTIONr_chiral_restr0.1560.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023060
X-RAY DIFFRACTIONr_nbd_refined0.2250.22016
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.221
X-RAY DIFFRACTIONr_mcbond_it1.2081.52747
X-RAY DIFFRACTIONr_mcangle_it1.88624322
X-RAY DIFFRACTIONr_scbond_it3.25131626
X-RAY DIFFRACTIONr_scangle_it4.6614.51368
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 68 -
Rwork0.225 1145 -
all-1213 -
obs--100 %

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