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- PDB-7dko: De novo design protein AM2M -

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Basic information

Entry
Database: PDB / ID: 7dko
TitleDe novo design protein AM2M
Componentsde novo designed protein AM2M
KeywordsDE NOVO PROTEIN / Monomer / Ferredoxin-like
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.6 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 25, 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 / Structure summary / Category: citation / citation_author / entity
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.pdbx_description
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: de novo designed protein AM2M
B: de novo designed protein AM2M
C: de novo designed protein AM2M


Theoretical massNumber of molelcules
Total (without water)28,2143
Polymers28,2143
Non-polymers00
Water23413
1
A: de novo designed protein AM2M


Theoretical massNumber of molelcules
Total (without water)9,4051
Polymers9,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: de novo designed protein AM2M


Theoretical massNumber of molelcules
Total (without water)9,4051
Polymers9,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: de novo designed protein AM2M


Theoretical massNumber of molelcules
Total (without water)9,4051
Polymers9,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.260, 58.620, 108.348
Angle α, β, γ (deg.)90.000, 91.340, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:7 or resseq 9:24 or (resid...
21(chain B and (resseq 1:7 or resseq 9:24 or (resid...
31(chain C and (resseq 1:7 or resseq 9:24 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVAL(chain A and (resseq 1:7 or resseq 9:24 or (resid...AA1 - 72 - 8
12PROPROALAALA(chain A and (resseq 1:7 or resseq 9:24 or (resid...AA9 - 2410 - 25
13GLUGLUGLUGLU(chain A and (resseq 1:7 or resseq 9:24 or (resid...AA2526
14ALAALALEULEU(chain A and (resseq 1:7 or resseq 9:24 or (resid...AA1 - 902 - 91
15ALAALALEULEU(chain A and (resseq 1:7 or resseq 9:24 or (resid...AA1 - 902 - 91
16ALAALALEULEU(chain A and (resseq 1:7 or resseq 9:24 or (resid...AA1 - 902 - 91
17ALAALALEULEU(chain A and (resseq 1:7 or resseq 9:24 or (resid...AA1 - 902 - 91
18ALAALALEULEU(chain A and (resseq 1:7 or resseq 9:24 or (resid...AA1 - 902 - 91
21ALAALAVALVAL(chain B and (resseq 1:7 or resseq 9:24 or (resid...BB1 - 72 - 8
22PROPROALAALA(chain B and (resseq 1:7 or resseq 9:24 or (resid...BB9 - 2410 - 25
23GLUGLUGLUGLU(chain B and (resseq 1:7 or resseq 9:24 or (resid...BB2526
24ALAALALEULEU(chain B and (resseq 1:7 or resseq 9:24 or (resid...BB1 - 902 - 91
25ALAALALEULEU(chain B and (resseq 1:7 or resseq 9:24 or (resid...BB1 - 902 - 91
26ALAALALEULEU(chain B and (resseq 1:7 or resseq 9:24 or (resid...BB1 - 902 - 91
31ALAALAVALVAL(chain C and (resseq 1:7 or resseq 9:24 or (resid...CC1 - 72 - 8
32PROPROALAALA(chain C and (resseq 1:7 or resseq 9:24 or (resid...CC9 - 2410 - 25
33GLUGLUGLUGLU(chain C and (resseq 1:7 or resseq 9:24 or (resid...CC2526
34ALAALALEULEU(chain C and (resseq 1:7 or resseq 9:24 or (resid...CC1 - 902 - 91
35ALAALALEULEU(chain C and (resseq 1:7 or resseq 9:24 or (resid...CC1 - 902 - 91
36ALAALALEULEU(chain C and (resseq 1:7 or resseq 9:24 or (resid...CC1 - 902 - 91

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Components

#1: Protein de novo designed protein AM2M


Mass: 9404.688 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.45 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 3.5M Sodium formate, 0.1M Sodium acetate trihydrate pH 4.6

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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 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.6→12.96 Å / Num. obs: 11773 / % possible obs: 98.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 12.42
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 549

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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: 2.6→12.958 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2892 549 4.66 %
Rwork0.2301 11224 -
obs0.2328 11773 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.38 Å2 / Biso mean: 50.3708 Å2 / Biso min: 8.56 Å2
Refinement stepCycle: final / Resolution: 2.6→12.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 0 13 1934
Biso mean---26.05 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071933
X-RAY DIFFRACTIONf_angle_d1.0272622
X-RAY DIFFRACTIONf_chiral_restr0.059335
X-RAY DIFFRACTIONf_plane_restr0.007339
X-RAY DIFFRACTIONf_dihedral_angle_d17.1881199
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1058X-RAY DIFFRACTION12.156TORSIONAL
12B1058X-RAY DIFFRACTION12.156TORSIONAL
13C1058X-RAY DIFFRACTION12.156TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6002-2.85930.37971720.3192715288798
2.8593-3.26730.34061360.27862802293899
3.2673-4.09470.32261200.229128242944100
4.0947-12.95770.20991210.182228833004100
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)
14.9501-0.4809-0.2685.5580.21665.3922-0.01560.3943-0.161-0.1041-0.0573-0.1090.26690.36870.0610.30180.0028-0.00650.2722-0.07370.24229.89881.194441.7775
25.75480.0162-1.08452.8768-1.63472.4848-0.1025-0.27440.32740.3743-0.0747-0.0048-0.11760.10280.09310.3438-0.0087-0.04110.2178-0.05670.24449.579411.28247.9922
34.8291-1.42741.38912.62591.58895.1519-0.1282-0.59470.79390.12340.395-0.456-0.52750.8941-0.14880.4050.00780.01160.5809-0.2140.524335.3073-7.340120.1483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 90)A1 - 90
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 90)B1 - 90
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 90)C1 - 90

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