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- PDB-5uvj: Serial Millisecond Crystallography of Membrane and Soluble Protei... -

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Basic information

Entry
Database: PDB / ID: 5uvj
TitleSerial Millisecond Crystallography of Membrane and Soluble Protein Micro-crystals using Synchrotron Radiation
ComponentsLysozyme C
KeywordsHYDROLASE
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMartin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. ...Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketawala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W.
Funding support United States, 8items
OrganizationGrant numberCountry
Flinn Foundation1991 United States
STC Program of the National Science Foundation through BioXFEL1231306 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095583 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108635 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM094618 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)Y1-CO-1020 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)Y1-GM-1104 United States
Department of Energy (DOE, United States)DE-AC02-06CH1135 United States
CitationJournal: IUCrJ / Year: 2017
Title: Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation.
Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / ...Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketwala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.7Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.8Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4615
Polymers14,3311
Non-polymers1294
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-41 kcal/mol
Surface area6500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.100, 79.100, 38.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 3
Details: 18 % (w/v) NaCl, 6 % (v/v) PEG 6000, 1 M sodium acetate pH 3.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.05→35 Å / Num. obs: 7164 / % possible obs: 99.79 % / Redundancy: 873.3 % / CC1/2: 0.978 / Net I/σ(I): 11.2
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 0.4 % / CC1/2: 0.436

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
CrystFEL0.6.2data scaling
Cheetahdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZIX

4zix


Resolution: 2.05→35 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.809 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 816 10.2 %RANDOM
Rwork0.22863 ---
obs0.23275 7164 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.203 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 2.05→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 4 18 1023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191025
X-RAY DIFFRACTIONr_bond_other_d0.0020.02940
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9031389
X-RAY DIFFRACTIONr_angle_other_deg0.96532140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6855128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1562350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29815166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2881511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021206
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02271
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1433.198515
X-RAY DIFFRACTIONr_mcbond_other2.1373.192514
X-RAY DIFFRACTIONr_mcangle_it3.254.794642
X-RAY DIFFRACTIONr_mcangle_other3.2554.8643
X-RAY DIFFRACTIONr_scbond_it3.5643.692510
X-RAY DIFFRACTIONr_scbond_other3.5513.691510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5645.366747
X-RAY DIFFRACTIONr_long_range_B_refined8.09431.0534390
X-RAY DIFFRACTIONr_long_range_B_other8.08931.0564389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 66 -
Rwork0.513 500 -
obs--98.78 %

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