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Basic information

Entry
Database: PDB / ID: 7dkk
TitleDe novo design protein XM2H
ComponentsDe novo design protein XM2H
KeywordsDE NOVO PROTEIN / Monomer / Ferredoxin-like
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsBin, H.
CitationJournal: Nature / Year: 2022
Title: A backbone-centred energy function of neural networks for protein design.
Authors: Huang, B. / Xu, Y. / Hu, X. / Liu, Y. / Liao, S. / Zhang, J. / Huang, C. / Hong, J. / Chen, Q. / Liu, H.
History
DepositionNov 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
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.title / _citation.year
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: De novo design protein XM2H
B: De novo design protein XM2H
C: De novo design protein XM2H
D: De novo design protein XM2H


Theoretical massNumber of molelcules
Total (without water)37,5954
Polymers37,5954
Non-polymers00
Water66737
1
A: De novo design protein XM2H


Theoretical massNumber of molelcules
Total (without water)9,3991
Polymers9,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo design protein XM2H


Theoretical massNumber of molelcules
Total (without water)9,3991
Polymers9,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: De novo design protein XM2H


Theoretical massNumber of molelcules
Total (without water)9,3991
Polymers9,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: De novo design protein XM2H


Theoretical massNumber of molelcules
Total (without water)9,3991
Polymers9,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.192, 63.712, 70.742
Angle α, β, γ (deg.)90.000, 101.620, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:10 or resseq 12 or (resid...
21(chain B and (resseq 2:10 or resseq 12:20 or resseq...
31(chain C and (resseq 2:10 or resseq 12 or (resid...
41(chain D and (resseq 2:10 or resseq 12 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 2:10 or resseq 12 or (resid...A2 - 10
121(chain A and (resseq 2:10 or resseq 12 or (resid...A12
131(chain A and (resseq 2:10 or resseq 12 or (resid...A13
141(chain A and (resseq 2:10 or resseq 12 or (resid...A1 - 89
151(chain A and (resseq 2:10 or resseq 12 or (resid...A1 - 89
161(chain A and (resseq 2:10 or resseq 12 or (resid...A1 - 89
171(chain A and (resseq 2:10 or resseq 12 or (resid...A1 - 89
211(chain B and (resseq 2:10 or resseq 12:20 or resseq...B2 - 10
221(chain B and (resseq 2:10 or resseq 12:20 or resseq...B12 - 20
231(chain B and (resseq 2:10 or resseq 12:20 or resseq...B22 - 25
241(chain B and (resseq 2:10 or resseq 12:20 or resseq...B0
251(chain B and (resseq 2:10 or resseq 12:20 or resseq...B52
261(chain B and (resseq 2:10 or resseq 12:20 or resseq...B1 - 89
271(chain B and (resseq 2:10 or resseq 12:20 or resseq...B1 - 89
281(chain B and (resseq 2:10 or resseq 12:20 or resseq...B1 - 89
311(chain C and (resseq 2:10 or resseq 12 or (resid...C2 - 10
321(chain C and (resseq 2:10 or resseq 12 or (resid...C12
331(chain C and (resseq 2:10 or resseq 12 or (resid...C13
341(chain C and (resseq 2:10 or resseq 12 or (resid...C1 - 89
351(chain C and (resseq 2:10 or resseq 12 or (resid...C1 - 89
361(chain C and (resseq 2:10 or resseq 12 or (resid...C1 - 89
371(chain C and (resseq 2:10 or resseq 12 or (resid...C1 - 89
411(chain D and (resseq 2:10 or resseq 12 or (resid...D2 - 10
421(chain D and (resseq 2:10 or resseq 12 or (resid...D12
431(chain D and (resseq 2:10 or resseq 12 or (resid...D13
441(chain D and (resseq 2:10 or resseq 12 or (resid...D1 - 89

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Components

#1: Protein
De novo design protein XM2H


Mass: 9398.665 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 2.0M Sodium chloride, 10%w/v Polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.1→13.03 Å / Num. obs: 23355 / % possible obs: 94.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 30.52 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.44
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 1193

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.1refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→13.024 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 1193 5.11 %
Rwork0.2257 22162 -
obs0.2277 23355 95.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.25 Å2 / Biso mean: 40.8803 Å2 / Biso min: 4.67 Å2
Refinement stepCycle: final / Resolution: 2.1→13.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 0 37 2657
Biso mean---27.19 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062644
X-RAY DIFFRACTIONf_angle_d0.9383577
X-RAY DIFFRACTIONf_chiral_restr0.053436
X-RAY DIFFRACTIONf_plane_restr0.006453
X-RAY DIFFRACTIONf_dihedral_angle_d18.7411615
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1219X-RAY DIFFRACTION15.398TORSIONAL
12B1219X-RAY DIFFRACTION15.398TORSIONAL
13C1219X-RAY DIFFRACTION15.398TORSIONAL
14D1219X-RAY DIFFRACTION15.398TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1001-2.18380.38381300.3329225589
2.1838-2.28270.31051200.3093236290
2.2827-2.40230.35621250.284236292
2.4023-2.55180.33251480.2707239294
2.5518-2.74710.28351270.2592246396
2.7471-3.02040.31311380.2562251897
3.0204-3.45030.2581230.2206258299
3.4503-4.32050.21741300.18922593100
4.3205-13.0240.2181520.17742635100
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)
12.9110.0605-1.27813.20191.10874.32440.3642-0.12620.3476-0.19720.1465-0.2052-0.6321-0.2429-0.45540.295-0.01230.03820.25450.01570.30350.660444.456356.6601
21.07921.93690.02033.547-0.2861.68920.3733-0.55790.0680.7719-0.6363-0.1450.05330.1210.20950.321-0.0819-0.03130.54130.00960.221335.937527.903765.6666
31.84080.10411.05692.3153-0.01873.89260.0391-0.2047-0.08580.06680.1157-0.07340.0832-0.1-0.18030.19060.01240.01820.15970.00670.207723.271717.530850.1185
42.0681-1.2332-1.21552.627-0.6521.7350.00270.08-0.0842-0.0502-0.00950.3510.1161-0.1646-0.04690.1889-0.0182-0.03350.16880.00170.255912.263834.118739.0256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 89)A1 - 89
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 89)B1 - 89
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 89)C1 - 89
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 89)D1 - 89

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