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- PDB-37tt: Crystal structure of Z4-C3ii -

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Basic information

Entry
Database: PDB / ID: 37tt
TitleCrystal structure of Z4-C3ii
ComponentsZ4 c3ii
KeywordsDE NOVO PROTEIN / protein design / diffusion / deep learning / protein-semiconductor / nano complexes
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsBera, A.K. / Pyles, H. / Saragovi, A. / Kang, A. / Baker, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Programmed mineralization of metal-oxides by de novo designed protein templates
Authors: Saragovi, A. / Pyles, H. / Bera, A.K. / Baker, D.
History
DepositionAug 5, 2026Deposition site: RCSB / Processing site: RCSB
SupersessionAug 19, 2026ID: 9CC4
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Z4 c3ii
B: Z4 c3ii
C: Z4 c3ii
D: Z4 c3ii
F: Z4 c3ii
E: Z4 c3ii


Theoretical massNumber of molelcules
Total (without water)147,7116
Polymers147,7116
Non-polymers00
Water181
1
A: Z4 c3ii
D: Z4 c3ii
E: Z4 c3ii


Theoretical massNumber of molelcules
Total (without water)73,8563
Polymers73,8563
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-48 kcal/mol
Surface area24590 Å2
MethodPISA
2
B: Z4 c3ii
C: Z4 c3ii
F: Z4 c3ii


Theoretical massNumber of molelcules
Total (without water)73,8563
Polymers73,8563
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-47 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.593, 68.520, 111.752
Angle α, β, γ (deg.)90.000, 90.884, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Z4 c3ii


Mass: 24618.578 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.88 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.03M Sodium fluoride, 0.03M Sodium bromide, 0.03 Sodium iodide, 0.0501M MOPS, 0.0499M Sodium HEPES, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 13, 2024 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.99→32.84 Å / Num. obs: 19063 / % possible obs: 90.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 92 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.06 / Net I/σ(I): 6.3
Reflection shellResolution: 2.99→3.15 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.265 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3022 / CC1/2: 0.523 / Rpim(I) all: 0.683 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→32.75 Å / SU ML: 0.526 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 35.4141
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2905 1906 10.04 %
Rwork0.2312 17085 -
obs0.237 18991 90.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.71 Å2
Refinement stepCycle: LAST / Resolution: 2.99→32.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9248 0 0 1 9249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00289283
X-RAY DIFFRACTIONf_angle_d0.492812504
X-RAY DIFFRACTIONf_chiral_restr0.03041571
X-RAY DIFFRACTIONf_plane_restr0.00381603
X-RAY DIFFRACTIONf_dihedral_angle_d21.24043468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.060.39331410.33371338X-RAY DIFFRACTION99.6
3.06-3.140.40341430.32251326X-RAY DIFFRACTION99.93
3.14-3.240.36861580.31781344X-RAY DIFFRACTION99.73
3.24-3.340.38851570.31211322X-RAY DIFFRACTION99.73
3.34-3.380.3452560.2943422X-RAY DIFFRACTION99.38
3.48-3.60.37391070.27931028X-RAY DIFFRACTION91.31
3.6-3.760.3033970.2586880X-RAY DIFFRACTION65.44
3.76-3.960.28661510.24081323X-RAY DIFFRACTION99.33
3.96-4.210.2871560.20381354X-RAY DIFFRACTION99.74
4.21-4.530.2521390.18931343X-RAY DIFFRACTION99.73
4.53-4.990.25571470.19761338X-RAY DIFFRACTION99.6
4.99-5.710.31671530.25061364X-RAY DIFFRACTION99.54
5.71-7.170.34171450.27171343X-RAY DIFFRACTION99.6
7.18-32.750.22821560.1871360X-RAY DIFFRACTION96.38
Refinement TLS params.Method: refined / Origin x: 7.9207501048035 Å / Origin y: 16.825581447804 Å / Origin z: 28.041305963823 Å
111213212223313233
T0.54810607260926 Å2-0.019522419708807 Å20.017319105650016 Å2-0.59340657760116 Å20.048731536009641 Å2--0.56461656273856 Å2
L0.35974494719921 °2-0.2200759403838 °20.12068539338405 °2-1.1494933636787 °20.37790136398382 °2--0.44124451971529 °2
S-0.019921100044342 Å °-0.062857244950297 Å °0.034801438025857 Å °-0.091467347286164 Å °0.011598498525888 Å °0.16173893733233 Å °-0.027052145938021 Å °0.012432395140823 Å °0.050872914457621 Å °
Refinement TLS groupSelection details: all

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