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- PDB-4dnh: Crystal structure of hypothetical protein SMc04132 from Sinorhizo... -

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Basic information

Entry
Database: PDB / ID: 4dnh
TitleCrystal structure of hypothetical protein SMc04132 from Sinorhizobium meliloti 1021
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-BIOLOGY / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC
Function / homologyProtein of unknown function DUF993 / Protein of unknown function (DUF993) / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Dihydrodipicolinate synthase family protein
Function and homology information
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.5 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein SMc04132 from Sinorhizobium meliloti 1021
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0673
Polymers43,8831
Non-polymers1842
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.291, 75.291, 139.518
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Uncharacterized protein


Mass: 43883.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: NP_384226.1, R00120, SMc04132 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q92T60
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.72 % / Mosaicity: 0.412 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3000, 0.1 M Tris, pH 7.0, 0.2 M Ca(OAc), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 13.64 / Number: 104452 / Rmerge(I) obs: 0.121 / Χ2: 1.33 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 27266 / % possible obs: 99.9
ReflectionResolution: 2.501→50 Å / Num. obs: 16435 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.121 / Χ2: 1.325 / Net I/av σ(I): 13.635 / Net I/σ(I): 7.1 / Num. measured all: 104452
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.501-2.643.80.98113360.8881100
2.64-2.693.80.86913750.8981100
2.69-2.743.80.75113500.8891100
2.74-2.83.80.67413810.9091100
2.8-2.863.80.5613480.9681100
2.86-2.933.80.46313730.9661100
2.93-33.80.37213540.9441100
3-3.083.90.32613970.9721100
3.08-3.173.90.29213540.9871100
3.17-3.283.90.21713610.9871100
3.28-3.393.90.17413551.1251100
3.39-3.533.80.13913831.1661100
3.53-3.693.90.1213511.431100
3.69-3.883.90.09913571.7161100
3.88-4.133.80.08413701.713199.9
4.13-4.453.80.0813702.268199.9
4.45-4.893.80.06413571.967199.8
4.89-5.63.70.06413541.7331100
5.6-7.053.90.06313791.788199.7
7.05-503.80.04413612.244198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.99 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.2 Å
Translation2.5 Å41.2 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2113 / WRfactor Rwork: 0.1524 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8625 / SU B: 18.083 / SU ML: 0.198 / SU R Cruickshank DPI: 0.4285 / SU Rfree: 0.2715 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.428 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 831 5.1 %RANDOM
Rwork0.1739 15573 --
obs0.1773 16404 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.66 Å2 / Biso mean: 54.5714 Å2 / Biso min: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 12 95 3067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193039
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9814115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6545385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90722.889135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94815460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9581528
X-RAY DIFFRACTIONr_chiral_restr0.090.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212320
LS refinement shellResolution: 2.501→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 62 -
Rwork0.262 1003 -
all-1065 -
obs--99.53 %
Refinement TLS params.Method: refined / Origin x: 40.5371 Å / Origin y: 7.986 Å / Origin z: 4.3952 Å
111213212223313233
T0.2541 Å2-0.1543 Å2-0.0388 Å2-0.098 Å20.0409 Å2--0.1603 Å2
L1.0063 °2-0.3012 °2-0.1017 °2-1.9578 °2-0.0025 °2--1.5359 °2
S-0.1931 Å °0.1279 Å °0.029 Å °-0.275 Å °0.2276 Å °0.264 Å °0.0011 Å °-0.0352 Å °-0.0345 Å °

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