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- PDB-6lfh: X-ray crystal structure of chemically synthesized human lysozyme -

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Basic information

Entry
Database: PDB / ID: 6lfh
TitleX-ray crystal structure of chemically synthesized human lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / Human lysozyme / chemical protein synthesis / one-pot native chemical ligation
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 Å
AuthorsKar, A. / Das, A. / Mandal, K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)IA/I/15/1/501847 India
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Efficient Chemical Protein Synthesis using Fmoc-Masked N-Terminal Cysteine in Peptide Thioester Segments.
Authors: Kar, A. / Mannuthodikayil, J. / Singh, S. / Biswas, A. / Dubey, P. / Das, A. / Mandal, K.
History
DepositionDec 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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_symmetry / _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_conn.ptnr2_symmetry
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9799
Polymers14,7211
Non-polymers2598
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-16 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.950, 56.410, 61.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C


Mass: 14720.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical Synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P61626, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Lysozyme sample (14 mg/mL) in 2.5 mM HEPES, 0.12 M lithium chloride mixed with reservoir solution containing 30 mM sodium phosphate, 2.5 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.34 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Jul 5, 2019 / Details: AXO MIRRORS for GALLIUM K-APLHA
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.46→30.61 Å / Num. obs: 19745 / % possible obs: 96.9 % / Redundancy: 9.228 % / Biso Wilson estimate: 21.355 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.047 / Χ2: 0.985 / Net I/σ(I): 31.37 / Num. measured all: 182201 / Scaling rejects: 52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.46-1.53.3520.7042.033523151210510.7240.83869.5
1.5-1.544.4840.4534.36063142213520.9310.51495.1
1.54-1.594.850.3296.326679140013770.9540.36998.4
1.59-1.645.0410.258.536841137413570.9740.27998.8
1.64-1.695.5870.17712.237252131212980.9880.19598.9
1.69-1.756.3260.14715.538103128512810.9910.16199.7
1.75-1.818.6170.11621.9810737125212460.9970.12399.5
1.81-1.8911.7690.10427.5313876118211790.9980.10999.7
1.89-1.9713.1060.07834.4215124115511540.9990.08199.9
1.97-2.0713.1020.06240.4514386110110980.9990.06499.7
2.07-2.1813.0780.0546.7213928106510650.9990.052100
2.18-2.3112.8240.04749.3126969909900.9990.049100
2.31-2.4712.5920.04352.8117239329310.9990.04599.9
2.47-2.6712.110.04253.38106088808760.9990.04499.5
2.67-2.9210.7160.03954.2185418117970.9990.04198.3
2.92-3.279.6720.03857.0772067497450.9990.0499.5
3.27-3.7813.430.0369.61893166966510.03199.4
3.78-4.6213.3290.02969.9575715685680.9990.03100
4.62-6.5412.6670.03165.64573845445310.03299.8
6.54-30.6110.210.0315926752722620.9990.03296.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXv1.17.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NWD

2nwd


Resolution: 1.46→30.61 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1957 989 5.01 %
Rwork0.1617 18735 -
obs0.1634 19724 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.05 Å2 / Biso mean: 19.1047 Å2 / Biso min: 7.58 Å2
Refinement stepCycle: final / Resolution: 1.46→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 8 213 1250
Biso mean--21.04 31.4 -
Num. residues----130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.46-1.540.2941180.27532203232181
1.54-1.640.24851410.19442703284499
1.64-1.760.19381420.15852696283899
1.76-1.940.19021490.15827192868100
1.94-2.220.17681480.14927432891100
2.22-2.80.21521390.16627892928100
2.8-30.610.17761520.15122882303499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.098-0.51010.35272.91120.97222.358-0.0768-0.18470.0010.19090.00760.20550.0293-0.0430.04410.075-0.00110.01050.09290.01650.051-11.6111.2462-4.1523
20.83440.2862-0.00982.39130.20131.62630.0562-0.0453-0.0357-0.0165-0.02410.0072-0.0715-0.0926-0.01160.07660.00980.0060.08940.00630.0729-6.275419.0347-11.8024
31.9075-0.5556-2.42060.21430.72574.5086-0.15510.2533-0.109-0.1664-0.07850.00850.2827-0.11040.20130.2193-0.01730.03160.1814-0.00720.1304-6.74854.29-23.2154
42.1639-0.7381-0.53971.40590.76161.16810.24770.14020.3613-0.33190.0029-0.4472-0.17490.0772-0.19530.1751-0.0050.06530.1232-0.00270.16393.13057.2217-22.4606
50.8296-0.24760.50451.9123-0.11080.8772-0.05110.06820.084-0.13210.0301-0.1436-0.0564-0.00340.02030.10920.00030.01060.11040.00560.0916-3.709516.4217-17.1616
61.5323-0.714-0.45944.74570.09772.57690.1725-0.06550.3586-0.0745-0.06450.3144-0.6206-0.5002-0.06990.21020.05910.03930.1976-0.00050.2089-17.177221.9049-6.383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'X' and (resid 1 through 14 )X1 - 14
2X-RAY DIFFRACTION2chain 'X' and (resid 15 through 36 )X15 - 36
3X-RAY DIFFRACTION3chain 'X' and (resid 37 through 50 )X37 - 50
4X-RAY DIFFRACTION4chain 'X' and (resid 51 through 79 )X51 - 79
5X-RAY DIFFRACTION5chain 'X' and (resid 80 through 121 )X80 - 121
6X-RAY DIFFRACTION6chain 'X' and (resid 122 through 130 )X122 - 130

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