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- PDB-3ib6: Crystal structure of an uncharacterized protein from Listeria mon... -

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Basic information

Entry
Database: PDB / ID: 3ib6
TitleCrystal structure of an uncharacterized protein from Listeria monocytogenes serotype 4b
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyHAD superfamily/HAD-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBonanno, J.B. / Gilmore, M. / Bain, K.T. / Do, J. / Ozyurt, S. / 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 Listeria monocytogenes serotype 4b
Authors: Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Do, J. / Ozyurt, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)85,8984
Polymers85,8984
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-43 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.122, 125.970, 73.385
Angle α, β, γ (deg.)90.000, 103.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 21474.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: Clip81459 / Gene: Lm4b_00283 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1KYJ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 16% PEG 3350, 100mM ammonium chloride, pH 7.0, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.2→38.101 Å / Num. all: 36871 / Num. obs: 36797 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 6.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5370 / Rsym value: 0.463 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 1.037 / WRfactor Rwork: 1.406 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.745 / SU B: 8.061 / SU ML: 0.206 / SU R Cruickshank DPI: 0.336 / SU Rfree: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.336 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1849 5 %RANDOM
Rwork0.218 ---
obs0.221 36729 99.86 %-
all-36780 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 88.61 Å2 / Biso mean: 52.616 Å2 / Biso min: 35.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20.29 Å2
2---1.11 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 0 119 5714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225722
X-RAY DIFFRACTIONr_bond_other_d0.0010.023694
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9667824
X-RAY DIFFRACTIONr_angle_other_deg0.95439135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88125.65246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58715944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.051516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021043
X-RAY DIFFRACTIONr_mcbond_it0.7451.53587
X-RAY DIFFRACTIONr_mcbond_other0.1581.51410
X-RAY DIFFRACTIONr_mcangle_it1.3725853
X-RAY DIFFRACTIONr_scbond_it2.04232135
X-RAY DIFFRACTIONr_scangle_it3.2624.51971
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 125 -
Rwork0.346 2558 -
all-2683 -
obs-2558 100 %

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