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- PDB-8h43: Crystal structure of PHF1 Tudor domain in complex with hit 1 -

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Basic information

Entry
Database: PDB / ID: 8h43
TitleCrystal structure of PHF1 Tudor domain in complex with hit 1
ComponentsPHD finger protein 1
KeywordsTRANSCRIPTION / Complex / inhibitor
Function / homology
Function and homology information


methylated histone binding / metal ion binding / nucleus
Similarity search - Function
: / : / PHD finger protein 1 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. ...: / : / PHD finger protein 1 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
2-[(3S)-piperidin-3-yl]-1,3-benzoxazole / PHD finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, Y. / Ruan, K.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21874123 China
National Natural Science Foundation of China (NSFC)32090040 China
CitationJournal: To be published
Title: Crystal structure of PHF1 Tudor domain in complex with hit 1
Authors: Liu, Y. / Ruan, K.
History
DepositionOct 10, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 1
B: PHD finger protein 1
C: PHD finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6466
Polymers21,0393
Non-polymers6073
Water70339
1
A: PHD finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2152
Polymers7,0131
Non-polymers2021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHD finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2152
Polymers7,0131
Non-polymers2021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHD finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2152
Polymers7,0131
Non-polymers2021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.718, 42.718, 401.905
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PHD finger protein 1 /


Mass: 7012.993 Da / Num. of mol.: 3 / Fragment: Tudor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9PQZ5
#2: Chemical ChemComp-1HI / 2-[(3S)-piperidin-3-yl]-1,3-benzoxazole


Mass: 202.252 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H14N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M sodium citrate, 2 M ammonium sulfate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→36.99 Å / Num. obs: 10935 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.042 / Rrim(I) all: 0.133 / Net I/σ(I): 13.4 / Num. measured all: 111123 / Scaling rejects: 479
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.399.70.9321078011090.8180.3130.9852.4100
8.61-36.996.90.11220763020.9910.0430.1223.599.2

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Processing

Software
NameVersionClassification
SCALA0.7.7data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HCZ

4hcz


Resolution: 2.3→19.921 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2889 523 4.85 %
Rwork0.2539 10254 -
obs0.2557 10777 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.05 Å2 / Biso mean: 68.8496 Å2 / Biso min: 27.75 Å2
Refinement stepCycle: final / Resolution: 2.3→19.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 45 39 1393
Biso mean--63.68 54.4 -
Num. residues----171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3002-2.53130.35591440.30542435
2.5313-2.89660.35241150.29752491
2.8966-3.64580.27571390.26182543
3.6458-100.2731250.23572785
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)
13.4412-5.1139-5.69367.67638.41469.598-0.6486-0.1976-0.58590.1320.27580.0652-0.0111-0.33970.2030.6150.05960.10491.0579-0.08990.6519-4.82968.6384-22.0817
22.2412-0.7164-2.36262.02610.99096.07520.30370.7230.1275-0.17580.0817-0.221-0.69240.4347-0.48880.49930.0160.15190.6289-0.30970.52632.914914.1199-19.1361
33.9255-2.0825-2.09273.34720.43831.6285-0.12820.8164-0.7184-0.0294-0.15090.49220.155-0.53850.26560.6292-0.04520.11181.8319-0.9621.234826.44944.5904-22.0331
40.07350.08360.1410.10050.15940.27070.0875-0.10990.0502-0.15920.3085-0.4523-0.3530.75360.12930.583-0.36130.19041.22-0.76190.874619.838214.2509-25.7253
54.17012.9825-1.0356.9265-3.21053.0172-0.1167-0.0069-0.2883-0.42650.1119-0.4199-0.34821.1214-0.07840.788-0.14650.16791.3656-0.59950.874219.212612.5318-19.4584
63.4662-0.6068-2.93761.34171.21712.89190.13760.2621-0.0405-0.06240.2171-0.262-0.02140.56280.07030.4748-0.12710.23131.2719-0.72320.950319.63089.5919-25.3752
73.57242.459-0.19244.4537-0.02743.90970.39190.008-0.14460.611-0.1902-0.9292-0.49860.2462-0.21710.43840.0746-0.01780.3966-0.2430.64412.264611.099-2.3763
83.52082.2381-2.5356.1297-0.79022.18420.0269-0.3147-0.6850.6285-0.246-1.18340.2830.90770.19670.45920.0771-0.08810.5017-0.17680.68564.09547.86212.2705
96.58434.4839-3.79976.4747-3.12116.24350.7963-0.45480.06011.2242-0.2794-0.53150.20040.2856-0.47550.5144-0.0402-0.12910.4988-0.2490.6101-2.46465.46152.6647
104.29921.90011.79253.87272.08733.4340.11340.3444-0.63170.29180.0719-0.51520.00470.61990.1210.3679-0.1396-0.13260.7968-0.39410.71475.485113.5162-4.8252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 35 )A27 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 86 )A36 - 86
3X-RAY DIFFRACTION3chain 'B' and (resid 28 through 35 )B28 - 35
4X-RAY DIFFRACTION4chain 'B' and (resid 36 through 55 )B36 - 55
5X-RAY DIFFRACTION5chain 'B' and (resid 56 through 69 )B56 - 69
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 83 )B70 - 83
7X-RAY DIFFRACTION7chain 'C' and (resid 29 through 45 )C29 - 45
8X-RAY DIFFRACTION8chain 'C' and (resid 46 through 65 )C46 - 65
9X-RAY DIFFRACTION9chain 'C' and (resid 66 through 74 )C66 - 74
10X-RAY DIFFRACTION10chain 'C' and (resid 75 through 83 )C75 - 83

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