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- PDB-3wu9: Spatiotemporal development of soaked protein crystal; derivative ... -

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Basic information

Entry
Database: PDB / ID: 3wu9
TitleSpatiotemporal development of soaked protein crystal; derivative 1580 sec
ComponentsLysozyme C
KeywordsHYDROLASE / HEN EGG WHITE LYSOZYME (HEWL) / BACTERIAL CELL WALL LYSIS
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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
DepositionApr 23, 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.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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3076
Polymers14,3311
Non-polymers9755
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lysozyme C
hetero molecules

A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,61312
Polymers28,6622
Non-polymers1,95110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1910 Å2
ΔGint-153 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.269, 79.269, 37.823
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-301-

PT4

21A-303-

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: 1,4-BETA-N-ACETYLMURAMIDASE C, 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.: 5 / Source method: obtained synthetically / Formula: Pt
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE ORIGINAL NUMBERs OF HOHs HAVE BEEN RENUMBERED. FOR EXAMPLE, HOH(130, CHAIN A) HAS BEEN CHANGED ...THE ORIGINAL NUMBERs OF HOHs HAVE BEEN RENUMBERED. FOR EXAMPLE, HOH(130, CHAIN A) HAS BEEN CHANGED TO HOH(301, CHAIN A). ORIGINAL RENUMBERED HOH(130, CHAIN A) HOH(401, CHAIN A). HOH(131, CHAIN A) HOH(402, CHAIN A). HOH(132, CHAIN A) HOH(403, CHAIN A). HOH(133, CHAIN A) HOH(404, CHAIN A). HOH(134, CHAIN A) HOH(405, CHAIN A). HOH(135, CHAIN A) HOH(406, CHAIN A). HOH(136, CHAIN A) HOH(407, CHAIN A). HOH(137, CHAIN A) HOH(408, CHAIN A). HOH(138, CHAIN A) HOH(409, CHAIN A). HOH(139, CHAIN A) HOH(410, CHAIN A). HOH(140, CHAIN A) HOH(411, CHAIN A). HOH(142, CHAIN A) HOH(412, CHAIN A). HOH(143, CHAIN A) HOH(413, CHAIN A). HOH(144, CHAIN A) HOH(414, CHAIN A). HOH(145, CHAIN A) HOH(415, CHAIN A). HOH(146, CHAIN A) HOH(416, CHAIN A). HOH(147, CHAIN A) HOH(417, CHAIN A). HOH(148, CHAIN A) HOH(418, CHAIN A). HOH(149, CHAIN A) HOH(419, CHAIN A). HOH(150, CHAIN A) HOH(420, CHAIN A). HOH(151, CHAIN A) HOH(421, CHAIN A). HOH(152, CHAIN A) HOH(422, CHAIN A). HOH(154, CHAIN A) HOH(423, CHAIN A). HOH(155, CHAIN A) HOH(424, CHAIN A). HOH(156, CHAIN A) HOH(425, CHAIN A). HOH(157, CHAIN A) HOH(426, CHAIN A). HOH(158, CHAIN A) HOH(427, CHAIN A). HOH(159, CHAIN A) HOH(428, CHAIN A). HOH(160, CHAIN A) HOH(429, CHAIN A). HOH(161, CHAIN A) HOH(430, CHAIN A). HOH(162, CHAIN A) HOH(431, CHAIN A). HOH(163, CHAIN A) HOH(432, CHAIN A). HOH(166, CHAIN A) HOH(433, CHAIN A). HOH(167, CHAIN A) HOH(434, CHAIN A). HOH(168, CHAIN A) HOH(435, CHAIN A). HOH(170, CHAIN A) HOH(436, CHAIN A). HOH(171, CHAIN A) HOH(437, CHAIN A). HOH(172, CHAIN A) HOH(438, CHAIN A). HOH(173, CHAIN A) HOH(439, CHAIN A). HOH(175, CHAIN A) HOH(440, CHAIN A). HOH(176, CHAIN A) HOH(441, CHAIN A). HOH(178, CHAIN A) HOH(442, CHAIN A). HOH(181, CHAIN A) HOH(443, CHAIN A). HOH(183, CHAIN A) HOH(444, CHAIN A). HOH(187, CHAIN A) HOH(445, CHAIN A). HOH(190, CHAIN A) HOH(446, CHAIN A). HOH(191, CHAIN A) HOH(447, CHAIN A). HOH(192, CHAIN A) HOH(448, CHAIN A). HOH(195, CHAIN A) HOH(449, CHAIN A). HOH(197, CHAIN A) HOH(450, CHAIN A). HOH(200, CHAIN A) HOH(451, CHAIN A). HOH(201, CHAIN A) HOH(452, CHAIN A). HOH(205, CHAIN A) HOH(453, CHAIN A). HOH(208, CHAIN A) HOH(454, CHAIN A). HOH(209, CHAIN A) HOH(455, CHAIN A). HOH(210, CHAIN A) HOH(456, CHAIN A). HOH(218, CHAIN A) HOH(457, CHAIN A). HOH(220, CHAIN A) HOH(458, CHAIN A). HOH(223, CHAIN A) HOH(459, CHAIN A). HOH(233, CHAIN A) HOH(460, CHAIN A). HOH(239, CHAIN A) HOH(461, CHAIN A). HOH(250, CHAIN A) HOH(462, CHAIN A). HOH(251, CHAIN A) HOH(463, CHAIN A). HOH(252, CHAIN A) HOH(464, CHAIN A). HOH(261, CHAIN A) HOH(465, CHAIN A). HOH(277, CHAIN A) HOH(466, 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: 40.66 %
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: 8609 / Num. obs: 8575 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rsym value: 0.083 / Net I/σ(I): 22.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 417 / Rsym value: 0.285 / % 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: PDB ENTRY 2LYM

2lym


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.308 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20713 403 4.7 %RANDOM
Rwork0.17565 ---
all0.17711 8577 --
obs0.17711 8553 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å20 Å2
2---0.26 Å20 Å2
3---0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.153 Å0.188 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 5 66 1072
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_deg1.5451.9031389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7422350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02115166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8231511
X-RAY DIFFRACTIONr_chiral_restr0.1120.2144
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_it1.6231.717515
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6292.559642
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2522.208510
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.56615.4171608
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 29 -
Rwork0.179 582 -
obs-611 99.84 %

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