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- PDB-3wpl: SPATIOTEMPORAL DEVELOPMENT of SOAKED PROTEIN CRYSTAL; 2510 SEC -

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Basic information

Entry
Database: PDB / ID: 3wpl
TitleSPATIOTEMPORAL DEVELOPMENT of SOAKED PROTEIN CRYSTAL; 2510 SEC
ComponentsLysozyme C
KeywordsHYDROLASE / BACTERIAL CELL WALL LYSIS
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 / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsMizutani, R. / Saiga, R.
CitationJournal: Sci Rep / Year: 2014
Title: Spatiotemporal development of soaked protein crystal
Authors: Mizutani, R. / Shimizu, Y. / Saiga, R. / Ueno, G. / Nakamura, Y. / Takeuchi, A. / Uesugi, K. / Suzuki, Y.
History
DepositionJan 12, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,9164
Polymers14,3311
Non-polymers5853
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.303, 79.303, 37.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-201-

PT4

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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 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-PT4 / PLATINUM (IV) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE ORIGINAL NUMBERs OF HOHs HAVE BEEN RENUMBERED. ORIGINAL RENUMBERED PT (303, CHAIN C) PT (201, ...THE ORIGINAL NUMBERs OF HOHs HAVE BEEN RENUMBERED. ORIGINAL RENUMBERED PT (303, CHAIN C) PT (201, CHAIN A). PT (304, CHAIN C) PT (202, CHAIN A). PT (305, CHAIN C) PT (203, CHAIN A). HOH(130, CHAIN A) HOH(301, CHAIN A). HOH(131, CHAIN A) HOH(302, CHAIN A). HOH(132, CHAIN A) HOH(303, CHAIN A). HOH(133, CHAIN A) HOH(304, CHAIN A). HOH(134, CHAIN A) HOH(305, CHAIN A). HOH(135, CHAIN A) HOH(306, CHAIN A). HOH(136, CHAIN A) HOH(307, CHAIN A). HOH(137, CHAIN A) HOH(308, CHAIN A). HOH(138, CHAIN A) HOH(309, CHAIN A). HOH(139, CHAIN A) HOH(310, CHAIN A). HOH(140, CHAIN A) HOH(311, CHAIN A). HOH(142, CHAIN A) HOH(312, CHAIN A). HOH(143, CHAIN A) HOH(313, CHAIN A). HOH(144, CHAIN A) HOH(314, CHAIN A). HOH(145, CHAIN A) HOH(315, CHAIN A). HOH(146, CHAIN A) HOH(316, CHAIN A). HOH(147, CHAIN A) HOH(317, CHAIN A). HOH(148, CHAIN A) HOH(318, CHAIN A). HOH(149, CHAIN A) HOH(319, CHAIN A). HOH(150, CHAIN A) HOH(320, CHAIN A). HOH(151, CHAIN A) HOH(321, CHAIN A). HOH(152, CHAIN A) HOH(322, CHAIN A). HOH(154, CHAIN A) HOH(323, CHAIN A). HOH(155, CHAIN A) HOH(324, CHAIN A). HOH(156, CHAIN A) HOH(325, CHAIN A). HOH(157, CHAIN A) HOH(326, CHAIN A). HOH(158, CHAIN A) HOH(327, CHAIN A). HOH(159, CHAIN A) HOH(328, CHAIN A). HOH(160, CHAIN A) HOH(329, CHAIN A). HOH(161, CHAIN A) HOH(330, CHAIN A). HOH(162, CHAIN A) HOH(331, CHAIN A). HOH(163, CHAIN A) HOH(332, CHAIN A). HOH(166, CHAIN A) HOH(333, CHAIN A). HOH(167, CHAIN A) HOH(334, CHAIN A). HOH(168, CHAIN A) HOH(335, CHAIN A). HOH(170, CHAIN A) HOH(336, CHAIN A). HOH(171, CHAIN A) HOH(337, CHAIN A). HOH(172, CHAIN A) HOH(338, CHAIN A). HOH(173, CHAIN A) HOH(339, CHAIN A). HOH(175, CHAIN A) HOH(340, CHAIN A). HOH(176, CHAIN A) HOH(341, CHAIN A). HOH(178, CHAIN A) HOH(342, CHAIN A). HOH(181, CHAIN A) HOH(343, CHAIN A). HOH(183, CHAIN A) HOH(344, CHAIN A). HOH(187, CHAIN A) HOH(345, CHAIN A). HOH(190, CHAIN A) HOH(346, CHAIN A). HOH(191, CHAIN A) HOH(347, CHAIN A). HOH(192, CHAIN A) HOH(348, CHAIN A). HOH(195, CHAIN A) HOH(349, CHAIN A). HOH(197, CHAIN A) HOH(350, CHAIN A). HOH(200, CHAIN A) HOH(351, CHAIN A). HOH(201, CHAIN A) HOH(352, CHAIN A). HOH(205, CHAIN A) HOH(353, CHAIN A). HOH(208, CHAIN A) HOH(354, CHAIN A). HOH(209, CHAIN A) HOH(355, CHAIN A). HOH(210, CHAIN A) HOH(356, CHAIN A). HOH(218, CHAIN A) HOH(357, CHAIN A). HOH(220, CHAIN A) HOH(358, CHAIN A). HOH(223, CHAIN A) HOH(359, CHAIN A). HOH(233, CHAIN A) HOH(360, CHAIN A). HOH(239, CHAIN A) HOH(361, CHAIN A). HOH(250, CHAIN A) HOH(362, CHAIN A). HOH(251, CHAIN A) HOH(363, CHAIN A). HOH(252, CHAIN A) HOH(364, CHAIN A). HOH(261, CHAIN A) HOH(365, CHAIN A). HOH(277, CHAIN A) HOH(366, CHAIN A).

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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: 293 K / Method: batch method / pH: 4.5
Details: 25mg/ml Lysozyme, 0.05M SODIUM ACETATE, 0.7M SODIUM CHLORIDE, pH 4.5, BATCH METHOD, temperature 293K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.07345 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2013
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07345 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 8614 / Num. obs: 8582 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rsym value: 0.082 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 7 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 412 / Rsym value: 0.29 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BSSdata collection
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2LYM

2lym


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.686 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22284 403 4.7 %RANDOM
Rwork0.17299 ---
all0.1753 8581 --
obs0.1753 8559 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å20 Å2
2---0.24 Å20 Å2
3---0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.164 Å0.185 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 3 66 1070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191025
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9031389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7652350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69815166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7031511
X-RAY DIFFRACTIONr_chiral_restr0.1180.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02794
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.6761.745515
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6882.599642
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2162.227510
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.50215.4641598
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 29 -
Rwork0.179 576 -
obs-605 99.83 %

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