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- PDB-7tun: Crystal structure analysis of human CKB complex with a covalent c... -

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Basic information

Entry
Database: PDB / ID: 7tun
TitleCrystal structure analysis of human CKB complex with a covalent compound
ComponentsCreatine kinase B-type
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / creatine kinase / ATP-binding / covalent inhibitor / cycteine modification / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


futile creatine cycle / Creatine metabolism / creatine kinase / phosphocreatine biosynthetic process / creatine kinase activity / RND3 GTPase cycle / substantia nigra development / ubiquitin protein ligase binding / mitochondrion / extracellular space ...futile creatine cycle / Creatine metabolism / creatine kinase / phosphocreatine biosynthetic process / creatine kinase activity / RND3 GTPase cycle / substantia nigra development / ubiquitin protein ligase binding / mitochondrion / extracellular space / extracellular exosome / ATP binding / plasma membrane / cytosol
Similarity search - Function
ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Chem-KLU / Creatine kinase B-type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.93 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of human CKB complex with a covalent compound
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Creatine kinase B-type
B: Creatine kinase B-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4574
Polymers89,9472
Non-polymers5092
Water1267
1
A: Creatine kinase B-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2282
Polymers44,9741
Non-polymers2551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Creatine kinase B-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2282
Polymers44,9741
Non-polymers2551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.240, 101.240, 160.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Creatine kinase B-type / Brain creatine kinase / B-CK / Creatine kinase B chain / Creatine phosphokinase B-type / CPK-B


Mass: 44973.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKB, CKBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12277, creatine kinase
#2: Chemical ChemComp-KLU / (2S)-4-(chloroacetyl)-3,4-dihydro-2H-1,4-benzoxazine-2-carboxamide


Mass: 254.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.7M Ammonium citrate, pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.93→85.68 Å / Num. obs: 18694 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 75.03 Å2 / Rpim(I) all: 0.083 / Rrim(I) all: 0.299 / Net I/σ(I): 9 / Num. measured all: 242855
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
2.93-2.9813.71.1127399320.7042.618
7.95-85.7211.128.21181010670.020.07

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
xia23.5.0data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DRE
Resolution: 2.93→71.59 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 876 4.71 %
Rwork0.2047 17729 -
obs0.2074 18605 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.9 Å2 / Biso mean: 80.7713 Å2 / Biso min: 47.67 Å2
Refinement stepCycle: final / Resolution: 2.93→71.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5671 0 54 7 5732
Biso mean--81.64 59.43 -
Num. residues----740
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.93-3.110.40091450.318928853030
3.11-3.350.36141420.252328853027
3.35-3.690.25011450.222629023047
3.69-4.230.2741440.188829543098
4.23-5.320.25151530.17229563109
5.32-71.590.221470.196931473294
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5642-0.1113-0.40161.2092-0.50440.6224-0.01850.59320.0319-0.35770.1070.083-0.61410.0096-00.7107-0.03880.01560.7559-0.09340.763418.064135.55194.6533
21.5187-0.2058-0.40240.9387-0.00711.83-0.0968-0.0376-0.2522-0.11680.0745-0.09640.261-0.0764-0.00030.5857-0.01390.04220.6615-0.00010.6355.805419.320718.5655
32.4521-0.44790.23540.4849-0.27781.7186-0.0596-0.0556-0.00470.03150.0443-0.035-0.1774-0.16380.00040.67420.00860.03810.5921-0.00810.608-2.827817.424222.9563
41.2925-0.128-0.91340.71650.48231.396-0.1285-0.60670.16440.17780.0444-0.0776-0.11350.1744-0.00060.62020.07030.0220.88150.01340.671913.182621.341541.159
53.21930.78740.78273.0962-1.12971.96950.04870.02050.0533-0.23040.0773-0.14270.07340.03130.00050.7598-0.1402-0.00420.92510.00850.6332-11.275934.2262-1.4617
62.2625-0.64740.50971.4177-0.0740.7562-0.2503-0.25750.4895-0.08510.21210.0173-0.4519-0.1731-00.94820.0160.01280.86930.0020.81181.263359.2031.7114
70.49770.59180.04741.6865-0.21970.3385-0.4099-0.15510.1882-0.26110.2030.3808-0.501-0.1613-0.00140.93860.1198-0.0881.177-0.08170.747-10.35857.7060.0413
80.39010.5457-0.3050.8807-0.3450.2748-0.6166-0.20530.19260.1462-0.07950.39-0.3868-0.28110.00011.10830.2426-0.2231.05650.04570.937-21.94566.51965.7072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 42 )A5 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 180 )A43 - 180
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 286 )A181 - 286
4X-RAY DIFFRACTION4chain 'A' and (resid 287 through 381 )A287 - 381
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 96 )B5 - 96
6X-RAY DIFFRACTION6chain 'B' and (resid 97 through 267 )B97 - 267
7X-RAY DIFFRACTION7chain 'B' and (resid 268 through 307 )B268 - 307
8X-RAY DIFFRACTION8chain 'B' and (resid 308 through 381 )B308 - 381

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