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- PDB-2dut: Crystal structure of a M-loop deletion variant of MENT in the nat... -

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Basic information

Entry
Database: PDB / ID: 2dut
TitleCrystal structure of a M-loop deletion variant of MENT in the native conformation
ComponentsHeterochromatin-associated protein MENT
KeywordsHYDROLASE INHIBITOR / SERINE PROTEASE INHIBITOR / SERPIN
Function / homology
Function and homology information


nucleate erythrocyte maturation / chromosome condensation / serine-type endopeptidase inhibitor activity / chromatin DNA binding / chromatin organization / chromatin / extracellular space / nucleoplasm
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Heterochromatin-associated protein MENT
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWhisstock, J.C. / Buckle, A.M. / McGowan, S. / Irving, J.A.
CitationJournal: Embo J. / Year: 2006
Title: X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation
Authors: McGowan, S. / Buckle, A.M. / Irving, J.A. / Ong, P.C. / Bashtannyk-Puhalovich, T.A. / Kan, W.T. / Henderson, K.N. / Bulynko, Y.A. / Popova, E.Y. / Smith, A.I. / Bottomley, S.P. / Rossjohn, J. ...Authors: McGowan, S. / Buckle, A.M. / Irving, J.A. / Ong, P.C. / Bashtannyk-Puhalovich, T.A. / Kan, W.T. / Henderson, K.N. / Bulynko, Y.A. / Popova, E.Y. / Smith, A.I. / Bottomley, S.P. / Rossjohn, J. / Grigoryev, S.A. / Pike, R.N. / Whisstock, J.C.
History
DepositionJul 26, 2006Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 8, 2006ID: 2H4S
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterochromatin-associated protein MENT
B: Heterochromatin-associated protein MENT
C: Heterochromatin-associated protein MENT
D: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)195,4244
Polymers195,4244
Non-polymers00
Water2,450136
1
A: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)48,8561
Polymers48,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)48,8561
Polymers48,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)48,8561
Polymers48,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)48,8561
Polymers48,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.559, 182.559, 96.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Heterochromatin-associated protein MENT / MENT


Mass: 48855.910 Da / Num. of mol.: 4 / Mutation: deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MENT-1 / Plasmid: pBAD-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O73790
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 4.76 Å3/Da / Density % sol: 74.16 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 1.7-1.9M AMMONIUM SULFATE, 0.1M SODIUM ACETATE, PH4.3-4.45, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 71951 / Num. obs: 68817 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 %
Rfree details: Random selection of twin-related reflection pairs
Rmerge(I) obs: 0.114 / Net I/σ(I): 10.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OVA

1ova


Resolution: 3→20 Å / Redundancy reflection obs: 2.5 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE DATA IS TWINNED. THE TWINNING OPERATOR IS (H,K,L)-> (H+K,-K,-L) AND THE ESTIMATED PARTIAL TWINNING FRACTION IS 0.44. THE TWINNED R-FACTORS ARE 29.7% (OBS), 29.7%(WORK) AND 32.4%(FREE). ...Details: THE DATA IS TWINNED. THE TWINNING OPERATOR IS (H,K,L)-> (H+K,-K,-L) AND THE ESTIMATED PARTIAL TWINNING FRACTION IS 0.44. THE TWINNED R-FACTORS ARE 29.7% (OBS), 29.7%(WORK) AND 32.4%(FREE). THE TWINNED BIN R-FACTORS ARE 36.0(WORK) AND 37.0(FREE). AT THIS TWINNING FRACTION, THE ESTIMATE IS LIKELY TO BE INACCURATE. HENCE, THE DATA WAS ARTIFICIALLY PERFECTLY TWINNED (=0.5) BY AVERAGING TWIN- RELATED REFLECTIONS. TO AVOID TEST-SET BIAS, TWIN-RELATED REFLECTIONS WERE RANDOMLY SELECTED IN PAIRS AND EXCLUDED FROM REFINEMENT FOR THE CALCULATION OF RFREE. CYCLES OF RIGID BODY REFINEMENT, SIMULATED ANNEALING, B-FACTOR REFINEMENT AND MAP BUILDING WERE UNDERTAKEN IN CNS USING THE XTAL_TWIN SUITE OF SCRIPTS.IN ORDER TO MAXIMISE THE OBSERVATION-TO-PARAMETER RATIO, STRICT CONSTRAINTS WERE APPLIED DURING REFINEMENT WITH CNS; AS SUCH, THE FOUR CHAINS ARE IDENTICAL AND RELATED PURELY BY COORDINATE TRANSFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.293 3090 -RANDOM
Rwork0.278 ---
obs0.278 68817 95.6 %-
all-71951 --
Solvent computationSolvent model: BULK / Bsol: 65.27 Å2 / ksol: 0.282 e/Å3
Displacement parametersBiso max: 103.164 Å2 / Biso mean: 41.015 Å2 / Biso min: 18.1339 Å2
Baniso -1Baniso -2Baniso -3
1--0.221 Å2-7.434 Å20 Å2
2---0.221 Å20 Å2
3---0.443 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10884 0 0 136 11020
LS refinement shellResolution: 3→3.1 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.35 384 5.4 %
Rwork0.334 --
all-7176 -
obs-7097 98.9 %

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