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- PDB-3mab: CRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM LISTERIA MON... -

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Basic information

Entry
Database: PDB / ID: 3mab
TitleCRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM LISTERIA MONOCYTOGENES, Triclinic FORM
Componentsuncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NYSGXRC / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homology5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsMadegowda, M. / Chruszcz, M. / Minor, W. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized protein from listeria monocytogenes
Authors: Madegowda, M. / Chruszcz, M. / Minor, W. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionApr 14, 2010ID: 3BQS
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.3Oct 6, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)21,0742
Polymers21,0742
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,5371
Polymers10,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,5371
Polymers10,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.062, 33.549, 40.784
Angle α, β, γ (deg.)83.24, 75.47, 89.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein uncharacterized protein


Mass: 10537.055 Da / Num. of mol.: 2 / Mutation: G27V, L50M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: F2365 / SEROTYPE 4B / Gene: 265669, LMOf2365_2733 / Plasmid: PSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q71W18
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.81 Å3/Da / Density % sol: 32.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M ammonium acetate, 0.1m Na citrate, 30% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 2, 2007 / Details: SGX-CAT
RadiationMonochromator: SGX CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. all: 50049 / Num. obs: 50049 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.4
Reflection shellResolution: 1.41→1.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.4 / % possible all: 82.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BQT

3bqt


Resolution: 1.42→16.87 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.541 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. This structure is a further-refined structure of an earlier PDB entry 3BQS, and this new refinement was done with anisotropic temperature factor
RfactorNum. reflection% reflectionSelection details
Rfree0.20633 1230 4.9 %RANDOM
Rwork0.1669 ---
obs0.16883 27987 89.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.326 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0.07 Å20.1 Å2
2---0.25 Å2-0.12 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.42→16.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 0 178 1542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221447
X-RAY DIFFRACTIONr_bond_other_d0.0010.021008
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9661951
X-RAY DIFFRACTIONr_angle_other_deg1.01132486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.565184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09525.31364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69215287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.027156
X-RAY DIFFRACTIONr_chiral_restr0.1170.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02266
X-RAY DIFFRACTIONr_mcbond_it1.1441.5888
X-RAY DIFFRACTIONr_mcbond_other0.331.5366
X-RAY DIFFRACTIONr_mcangle_it1.99721425
X-RAY DIFFRACTIONr_scbond_it3.3143559
X-RAY DIFFRACTIONr_scangle_it5.2514.5524
LS refinement shellResolution: 1.419→1.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 70 -
Rwork0.261 1460 -
obs--73.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1899-0.4559-0.5931.3774-0.08981.4739-0.0682-0.0532-0.08590.101-0.03070.00080.05650.03950.0990.04590.0072-0.01770.04180.00210.0470.0240.250.512
21.14810.81050.49442.53570.6241.2434-0.0693-0.00610.0059-0.15370.0072-0.01720.00620.03070.0620.04750.0269-0.01790.0535-0.00360.037515.093-0.28319.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 93
2X-RAY DIFFRACTION2B1 - 93

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