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- PDB-3nir: Crystal structure of small protein crambin at 0.48 A resolution -

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Basic information

Entry
Database: PDB / ID: 3nir
TitleCrystal structure of small protein crambin at 0.48 A resolution
ComponentsCrambin
KeywordsPLANT PROTEIN
Function / homology
Function and homology information


defense response / extracellular region
Similarity search - Function
Thionin-like / Thionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / Crambin / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCrambe hispanica (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS TO PDB ENTRY 1EJG / Resolution: 0.48 Å
AuthorsSchmidt, A. / Teeter, M. / Weckert, E. / Lamzin, V.S.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystal structure of small protein crambin at 0.48 A resolution
Authors: Schmidt, A. / Teeter, M. / Weckert, E. / Lamzin, V.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.
Authors: Jelsch, C. / Teeter, M.M. / Lamzin, V.S. / Pichon-Pesme, V. / Blessing, R.H. / Lecomte, C.
History
DepositionJun 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.6Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: Crambin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9235
Polymers4,7381
Non-polymers1844
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.329, 18.471, 40.769
Angle α, β, γ (deg.)90.00, 90.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Crambin


Mass: 4738.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Crambe hispanica (plant) / Strain: SUBSP. ABYSSINICA / References: UniProt: P01542
#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.7730.67
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% ethanol in water, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA II, DESYPETRA110.5498
SYNCHROTRONPETRA II, DESYPETRA120.5636
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJul 5, 2001
MAR CCD 165 mm2CCDFeb 25, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1diamond (111) - germanium (220)SINGLE WAVELENGTHMx-ray1
2diamond (111) - germanium (220)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.54981
20.56361
ReflectionResolution: 0.48→20 Å / Num. all: 156860 / Num. obs: 156860 / % possible obs: 97 % / Redundancy: 3.7 % / Biso Wilson estimate: 2.14 Å2 / Rsym value: 0.075 / Net I/σ(I): 9.7
Reflection shellResolution: 0.48→0.49 Å / Mean I/σ(I) obs: 1.5

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Processing

Software
NameClassification
MAR345data collection
MOPROrefinement
DENZOdata reduction
SCALEPACKdata scaling
SCALAdata scaling
RefinementMethod to determine structure: ISOMORPHOUS TO PDB ENTRY 1EJG
Starting model: PDB entry 1EJG

1ejg


Resolution: 0.48→20 Å / Isotropic thermal model: overall / Cross valid method: RFREE INITIALLY, FINAL STAGES NONE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: INITIAL REFINEMENT WITH REFMAC THEN SHELX, THEN MOPRO FOR MULTIPOLE REFINEMENT. ONLY DURING REFMAC CROSS VALIDATION WITH RFREE. IN THE LAST STAGES OF REFINEMENT THE SUM OF OCCUPANCIES FOR ...Details: INITIAL REFINEMENT WITH REFMAC THEN SHELX, THEN MOPRO FOR MULTIPOLE REFINEMENT. ONLY DURING REFMAC CROSS VALIDATION WITH RFREE. IN THE LAST STAGES OF REFINEMENT THE SUM OF OCCUPANCIES FOR THE MULTIPLE CONFORMERS WAS NOT CONSTRAINED TO 1.00 AND ONLY WEAK STEREOCHEMICAL RESTRAINTS WERE APPLIED. ALTHOUGH OVERALL SUCH REFINEMENT OF THE MULTIPLE CONFORMERS WENT FINE, THERE WAS SOME INSTABILITY - FOR EXAMPLE THE REFINEMENT OF THE TEMPERATURE FACTORS FOR CA AND C ATOMS OF THE THIRD CONFORMER OF TYR A 29 DID NOT CONVERGE AND WERE TRUNCATED TO THE VALUE OF 50. BULK SOLVENT MODELING METHOD USED:BULK SOLVENT ENVELOPE METHOD FC(MOL)+FC(BULK)
RfactorNum. reflection% reflectionSelection details
Rwork0.127 ---
obs0.127 156860 97 %-
all-156860 --
Rfree---random
Displacement parametersBiso mean: 4.12 Å2
Refinement stepCycle: LAST / Resolution: 0.48→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms341 0 12 98 451

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