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- PDB-7rgr: Lysozyme 056 from Deep neural language modeling -

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Basic information

Entry
Database: PDB / ID: 7rgr
TitleLysozyme 056 from Deep neural language modeling
ComponentsArtificial protein L056
KeywordsHYDROLASE / Lysozyme / designed proteins
Function / homologyLysozyme - #40 / Lysozyme / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsFraser, J.S. / Holton, J.M. / Olmos Jr., J.L. / Greene, E.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM123159 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124149 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124169 United States
CitationJournal: Nat.Biotechnol. / Year: 2023
Title: Large language models generate functional protein sequences across diverse families.
Authors: Madani, A. / Krause, B. / Greene, E.R. / Subramanian, S. / Mohr, B.P. / Holton, J.M. / Olmos Jr., J.L. / Xiong, C. / Sun, Z.Z. / Socher, R. / Fraser, J.S. / Naik, N.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Artificial protein L056
A: Artificial protein L056
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5294
Polymers38,2862
Non-polymers2432
Water46826
1
B: Artificial protein L056
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3502
Polymers19,1431
Non-polymers2071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Artificial protein L056
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1792
Polymers19,1431
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.150, 68.100, 95.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 2 through 167)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAASNC1 - 166
d_21ens_1ALAASNB1 - 166

NCS oper: (Code: givenMatrix: (-0.99007503263, 0.140529839986, 0.00167147725017), (0.140537704996, 0.990055018785, 0.00634139197371), (-0.000763699640964, 0.00651335944198, -0.999978496225)Vector: -1. ...NCS oper: (Code: given
Matrix: (-0.99007503263, 0.140529839986, 0.00167147725017), (0.140537704996, 0.990055018785, 0.00634139197371), (-0.000763699640964, 0.00651335944198, -0.999978496225)
Vector: -1.97108344926, 0.122004708997, 47.3327418722)

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Components

#1: Protein Artificial protein L056


Mass: 19143.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: lysozyme
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1 M CHES 9.5 pH, 30 %w/v PEG 3K

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Data collection

DiffractionMean temperature: 92.5 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11636 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2021 / Details: Pt/Rh mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11636 Å / Relative weight: 1
ReflectionResolution: 2.475→55.43 Å / Num. obs: 14751 / % possible obs: 99.9 % / Redundancy: 12.78 % / Biso Wilson estimate: 59.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.139 / Net I/av σ(I): 13.72 / Net I/σ(I): 13.72
Reflection shellResolution: 2.475→2.54 Å / Redundancy: 11.97 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 1088 / CC1/2: 0.721 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
BUCCANEER1.6.10model building
XDSFeb 5, 2021data reduction
XSCALEFeb 5, 2021data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: trRosetta prediction

Resolution: 2.48→55.43 Å / SU ML: 0.4536 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 31.926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2964 762 5.17 %
Rwork0.2589 13978 -
obs0.2608 14740 99.81 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.89 Å2
Refinement stepCycle: LAST / Resolution: 2.48→55.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 14 26 2704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392719
X-RAY DIFFRACTIONf_angle_d0.63243664
X-RAY DIFFRACTIONf_chiral_restr0.0464413
X-RAY DIFFRACTIONf_plane_restr0.0037461
X-RAY DIFFRACTIONf_dihedral_angle_d11.05041019
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.779894696822 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.670.38011550.34562731X-RAY DIFFRACTION99.76
2.67-2.930.30681570.29492750X-RAY DIFFRACTION99.93
2.93-3.360.36011400.30612770X-RAY DIFFRACTION99.97
3.36-4.230.271600.25162799X-RAY DIFFRACTION99.9
4.23-55.430.28031500.22832928X-RAY DIFFRACTION99.52
Refinement TLS params.Method: refined / Origin x: -0.219675069621 Å / Origin y: 11.8413365775 Å / Origin z: 23.7149049276 Å
111213212223313233
T0.417178132204 Å2-0.00939862924678 Å20.0150175396562 Å2-0.337962173381 Å2-0.0260455280895 Å2--0.498926219856 Å2
L0.619774365714 °2-0.0425927924702 °20.141893545396 °2-0.29918684394 °2-0.301661934929 °2--3.11273420859 °2
S-0.0483622549773 Å °-0.0222451717862 Å °-0.0260005021491 Å °0.0557450328277 Å °0.0143401030695 Å °-0.0121311131018 Å °0.10269741044 Å °0.00408711723389 Å °0.0260360668475 Å °
Refinement TLS groupSelection details: all

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