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- PDB-5hll: Re-refinement of 4g4a: room-temperature X-ray diffraction study o... -

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Basic information

Entry
Database: PDB / ID: 5hll
TitleRe-refinement of 4g4a: room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO.
ComponentsLysozyme C
KeywordsHYDROLASE / cisplatin / histidine / DMSO / Hen egg white lysozyme / raw diffraction images data
Function / homology
Function and homology information


Lactose synthesis / 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 ...Lactose synthesis / 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
AMMONIA / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHelliwell, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Citation
Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Re-refinement of 4g4a: room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO.
Authors: Tanley, S.W. / Schreurs, A.M. / Kroon-Batenburg, L.M. / Helliwell, J.R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Data collection
Category: diffrn_radiation_wavelength / diffrn_source / pdbx_audit_support
Item: _diffrn_source.source / _pdbx_audit_support.funding_organization
Revision 1.4Aug 8, 2018Group: Data collection / Database references
Category: citation / pdbx_database_related / pdbx_related_exp_data_set
Item: _citation.journal_abbrev / _pdbx_database_related.details / _pdbx_related_exp_data_set.data_reference
SupersessionDec 16, 2020ID: 4G4A
Revision 1.5Dec 16, 2020Group: Advisory / Derived calculations
Category: pdbx_database_PDB_obs_spr / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.6Jan 10, 2024Group: 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
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,01512
Polymers14,3311
Non-polymers68411
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-92 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.1443, 79.1443, 37.9968
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

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Protein , 1 types, 1 molecules A

#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 natural source / Details: Hen egg white lyysozyme with cisplatin with DMSO / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme

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Non-polymers , 6 types, 43 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#6: Chemical ChemComp-NH3 / AMMONIA / Ammonia


Mass: 17.031 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NH3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 4.7
Details: HEWL CO-CRYSTALLIZED WITH CISPLATIN, WITH 5% DMSO MEDIA IN 1 ML, 10% SODIUM CHLORIDE + 1 ML 0.04 M SODIUM ACETATE, PH 4.7, BATCH, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 25, 2012
RadiationMonochromator: CONFOCAL MIRROR OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.699→35.39 Å / Num. obs: 13804 / % possible obs: 99.68 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.9861835344 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 9.8
Reflection shellResolution: 1.699→1.728 Å / Redundancy: 4.5 % / Rmerge(I) obs: 2.428 / Mean I/σ(I) obs: 0.56 / % possible all: 93.86

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4g4a

4g4a
PDB Unreleased entry


Resolution: 1.7→35.39 Å / SU ML: 0.220931737624 / SU R Cruickshank DPI: 0.177 / Cross valid method: FREE R-VALUE / Phase error: 23.7110864462
RfactorNum. reflection% reflectionSelection details
Rfree0.224 703 5.20470866958 %Random
Rwork0.18 12804 --
obs0.182 13507 97.8626286046 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.3947691261 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 14 32 1047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01299721258661071
X-RAY DIFFRACTIONf_angle_d1.295635112941434
X-RAY DIFFRACTIONf_chiral_restr0.0539763548156148
X-RAY DIFFRACTIONf_plane_restr0.00685649835475189
X-RAY DIFFRACTIONf_dihedral_angle_d13.4617637632391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.83130.3128132493251410.289870598762415X-RAY DIFFRACTION94.4916820702
1.8313-2.01560.2965310150741390.2431422808512481X-RAY DIFFRACTION97.1089696071
2.0156-2.30720.2690215542561210.1876875599092556X-RAY DIFFRACTION98.4915378955
2.3072-2.90670.2428393948261440.1831394514552606X-RAY DIFFRACTION99.1705733862
2.9067-35.40210.1739240989531580.1447380249932746X-RAY DIFFRACTION99.8624484182

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