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- PDB-9nwn: Structure of minimal CRISPR polymerase bound to ApNHpp -

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Basic information

Entry
Database: PDB / ID: 9nwn
TitleStructure of minimal CRISPR polymerase bound to ApNHpp
ComponentsMCpol domain-containing protein
KeywordsIMMUNE SYSTEM / cyclase / palm domain / cyclic oligonucleotide / mCpol
Function / homologyMinimal CRISPR polymerase domain / minimal CRISPR polymerase domain / Chem-ZAN / MCpol domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDoherty, E.E. / Bolling, C.B. / Wilcox, X.E. / Doudna, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM153031 United States
CitationJournal: To Be Published
Title: Structure of minimal CRISPR polymerase bound to ApNHpp
Authors: Doherty, E.E. / Bolling, C.B. / Wilcox, X.E. / Doudna, J.A.
History
DepositionMar 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: MCpol domain-containing protein
A: MCpol domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1556
Polymers28,0942
Non-polymers1,0614
Water1,27971
1
B: MCpol domain-containing protein
hetero molecules

B: MCpol domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1556
Polymers28,0942
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2450 Å2
ΔGint-12 kcal/mol
Surface area10980 Å2
MethodPISA
2
A: MCpol domain-containing protein
hetero molecules

A: MCpol domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1556
Polymers28,0942
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2520 Å2
ΔGint-12 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.135, 56.769, 93.705
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-333-

HOH

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Components

#1: Protein MCpol domain-containing protein / Minimal CRISPR polymerase


Mass: 14046.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ECOR 31 / Gene: DU321_04150 / Production host: Escherichia coli BL21 (bacteria)
Variant (production host): F-ompT hsdSB(rB- mB-) gal dcm (DE3) pLysSRARE2 (CamR)
References: UniProt: A0A426EXS8
#2: Chemical ChemComp-ZAN / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Bicine pH 8.0, 15% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.28→48.55 Å / Num. obs: 12367 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 35.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.061 / Rrim(I) all: 0.159 / Net I/σ(I): 6.8
Reflection shellResolution: 2.28→2.37 Å / Num. unique obs: 1349 / CC1/2: 0.884 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→48.55 Å / SU ML: 0.2679 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.847
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2488 1229 10 %
Rwork0.2243 11064 -
obs0.2269 12293 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.86 Å2
Refinement stepCycle: LAST / Resolution: 2.28→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 64 71 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01791987
X-RAY DIFFRACTIONf_angle_d1.95852690
X-RAY DIFFRACTIONf_chiral_restr0.0857307
X-RAY DIFFRACTIONf_plane_restr0.0151332
X-RAY DIFFRACTIONf_dihedral_angle_d29.2555335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.370.28991350.28091214X-RAY DIFFRACTION99.78
2.37-2.480.26951360.26981221X-RAY DIFFRACTION99.41
2.48-2.610.29991340.25861222X-RAY DIFFRACTION99.34
2.61-2.770.32841350.27081209X-RAY DIFFRACTION98.1
2.77-2.990.2931350.25121225X-RAY DIFFRACTION99.27
2.99-3.290.26311380.2311237X-RAY DIFFRACTION99.71
3.29-3.760.26651330.22521196X-RAY DIFFRACTION94.59
3.76-4.740.1971340.18361197X-RAY DIFFRACTION94.6
4.74-48.550.21981490.20521343X-RAY DIFFRACTION99.14
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)
12.77651649553-2.6979740505-0.6100611862776.005024581570.6621713798673.86797007226-0.32514318692-0.1519638051130.393953152351-0.03657754166350.473782055849-1.25513223072-0.1654620212480.276110269378-0.2601641038260.423208224259-0.0359953250292-0.009114873025190.281787216804-0.001361684952860.3008512158976.4807439380631.4286474782-31.845571796
29.09173423954-7.38268873609-4.875166992366.861616480965.704982344966.03444034289-0.0928284326220.03231595332610.125533060733-0.792730686466-0.0682215386028-0.0973574420115-0.3787675274470.372930186549-0.002345084190990.498179674642-0.03442359039890.06786716626690.3174939521910.09379037270940.3095186334948.9083226517629.8985670606-42.8148760941
32.91908791576-0.7837039994190.6127235707790.634442010499-0.6961448733696.21793658350.02734998863880.0418472837833-0.032363954644-0.307814138581-0.0211169711403-0.3697108425210.1612429313330.3832685762850.02514299297170.436077631839-0.002631286425220.07282919308130.1927276104170.01309306415880.40204305080611.712917976816.1073144561-33.8192877371
43.19985700348-3.228811118730.2108123250173.80716769523-0.5080132622842.40458172015-0.5255884848990.327398999281-0.3809941126-0.141140064175-0.188998276555-0.1484844312710.0725917456977-0.0673735237823-0.4090861243520.943362955983-0.02341542966120.1458689399870.263995123022-0.02037672484130.4457055024-4.3375727587416.0826157167-11.7318683405
55.10805873101-1.18342273176-1.286902915115.63445057516-3.735513418484.209943074590.08305419769960.1905983124-0.2945341708940.3818514676620.3872554277941.360578536110.0794805648383-0.631810118493-0.2170563463810.778856012539-0.02014062522920.03814772420410.222122951371-0.02966223219160.40559134319-9.2449163746438.0915478573-15.0363778707
61.79118294962-0.623755691191-0.2685154409713.32197710737-3.191339957443.501844354190.0250190161335-0.2004241418590.1620127123880.2711940776980.06362257401860.7053661574930.0620953245469-0.0315207462973-0.038276394070.751210203363-0.09059272114620.08556182347740.267191529909-0.05990422389220.401518541539-8.7129229025126.5085176177-2.75812087213
71.84977794759-0.491962261135-1.252442526241.480436714980.2940034533682.49613138637-0.0674113969930.0193782528492-0.5275297586550.614945910281-0.0334797042750.6295352374890.371916551647-0.1461803243310.1930062725840.905879134323-0.1142984812940.05996893470980.2364364559050.0003064713839240.460050859063-6.3324425819912.0033027734-4.9002025318
84.896286720231.3132360242-5.082600071568.618749025224.374105198829.269411188080.1013990865250.314113526618-0.2819153807210.4211167410620.1882551609210.998754637701-1.33499292261-1.670982846840.04255454085910.4770507383880.1254663983930.008298061439730.64483579857-0.1053736533410.575261944557-15.769444511326.4904393933-11.2016909535
92.59166677136-1.02932226945-0.9793041963110.695336364131-0.07525797520332.77225026393-0.0562401668670.120842267068-0.5888802118780.665543088565-0.1654875326680.2126358227330.179374148423-0.009491801905680.2462688758480.561539873824-0.04064849743780.0601000869580.215346506106-0.006884982126580.391583186408-4.3262620065811.2058036826-18.1182094864
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 22 )AB1 - 221 - 22
22chain 'A' and (resid 23 through 47 )AB23 - 4723 - 47
33chain 'A' and (resid 48 through 120 )AB48 - 12048 - 120
44chain 'B' and (resid 1 through 9 )BA1 - 91 - 9
55chain 'B' and (resid 10 through 22 )BA10 - 2210 - 22
66chain 'B' and (resid 23 through 47 )BA23 - 4723 - 47
77chain 'B' and (resid 48 through 79 )BA48 - 7948 - 79
88chain 'B' and (resid 80 through 85 )BA80 - 8580 - 85
99chain 'B' and (resid 86 through 120 )BA86 - 12086 - 120

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