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- PDB-4fc1: Ultra-high resolution neutron structure of crambin at room-temperature -

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Basic information

Entry
Database: PDB / ID: 4fc1
TitleUltra-high resolution neutron structure of crambin at room-temperature
ComponentsCrambin
KeywordsUNKNOWN FUNCTION / H/D exchange / neutron structure
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
DEUTERATED WATER / Crambin
Similarity search - Component
Biological speciesCrambe hispanica subsp. abyssinica (Abyssinian crambe)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsKovalevsky, A.Y. / Chen, J.C.-H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography.
Authors: Chen, J.C. / Hanson, B.L. / Fisher, S.Z. / Langan, P. / Kovalevsky, A.Y.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Feb 28, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list ..._diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type
Revision 1.3Jun 6, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crambin


Theoretical massNumber of molelcules
Total (without water)4,7381
Polymers4,7381
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.795, 18.826, 41.042
Angle α, β, γ (deg.)90.00, 90.89, 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 subsp. abyssinica (Abyssinian crambe)
References: UniProt: P01542
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 290 K
Details: large crystals were obtained in 1mL crystallization drops containing 20-30mg/ml protein in 80% EtOH/H2O; the well solution was 60% EtOH/H2O; no mixing with well solution was done., VAPOR ...Details: large crystals were obtained in 1mL crystallization drops containing 20-30mg/ml protein in 80% EtOH/H2O; the well solution was 60% EtOH/H2O; no mixing with well solution was done., VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: LANSCE / Beamline: PCS / Wavelength: 0.7 - 6.0
DetectorType: HE3 POSITION SENSITIVE DETECTOR / Detector: AREA DETECTOR / Date: Oct 10, 2011
RadiationMonochromator: NONE / Protocol: LAUE / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
261
ReflectionResolution: 1.1→15.18 Å / Num. obs: 11122 / % possible obs: 78.8 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.231 / Net I/σ(I): 5.5
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 2 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 1.8 / % possible all: 65.8

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Processing

Software
NameVersionClassification
PCShome softwaredata collection
CNSrefinement
nCNSrefinement
SHELXrefinement
d*TREKdata reduction
LAUENORMdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→10 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.253 554 5 %RANDOM
all0.213 11102 --
obs0.211 ---
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms327 0 0 42 369
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONs_bond_d0.02
NEUTRON DIFFRACTIONs_angle_d0.028
NEUTRON DIFFRACTIONs_similar_dist
NEUTRON DIFFRACTIONs_from_restr_planes
NEUTRON DIFFRACTIONs_zero_chiral_vol
NEUTRON DIFFRACTIONs_non_zero_chiral_vol
NEUTRON DIFFRACTIONs_anti_bump_dis_restr
NEUTRON DIFFRACTIONs_rigid_bond_adp_cmpnt
NEUTRON DIFFRACTIONs_similar_adp_cmpnt
NEUTRON DIFFRACTIONs_approx_iso_adps

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