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- PDB-6wbj: High resolution crystal structure of mRECK(CC4) in fusion with en... -

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Basic information

Entry
Database: PDB / ID: 6wbj
TitleHigh resolution crystal structure of mRECK(CC4) in fusion with engineered MBP
ComponentsMaltodextrin-binding protein,Reversion-inducing cysteine-rich protein with Kazal motifs fusion
KeywordsSIGNALING PROTEIN / Wnt signaling / 4-helix bundle / extracellular domain / vascularization / blood-brain barrier / Maltose-binding protein
Function / homology
Function and homology information


regulation of establishment of blood-brain barrier / : / negative regulation of metalloendopeptidase activity / Post-translational modification: synthesis of GPI-anchored proteins / blood vessel maturation / : / metalloendopeptidase inhibitor activity / Wnt-protein binding / embryonic forelimb morphogenesis / Wnt signalosome ...regulation of establishment of blood-brain barrier / : / negative regulation of metalloendopeptidase activity / Post-translational modification: synthesis of GPI-anchored proteins / blood vessel maturation / : / metalloendopeptidase inhibitor activity / Wnt-protein binding / embryonic forelimb morphogenesis / Wnt signalosome / sprouting angiogenesis / endopeptidase inhibitor activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / regulation of angiogenesis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / embryo implantation / ATP-binding cassette (ABC) transporter complex / extracellular matrix organization / cell chemotaxis / negative regulation of cell migration / serine-type endopeptidase inhibitor activity / positive regulation of canonical Wnt signaling pathway / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane / plasma membrane
Similarity search - Function
Reversion-inducing cysteine-rich protein with Kazal motifs / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...Reversion-inducing cysteine-rich protein with Kazal motifs / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein / Reversion-inducing cysteine-rich protein with Kazal motifs
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.651 Å
Model detailsmouse RECK CC domain 4 in fusion with engineered Maltose Binding Protein
AuthorsChang, T.H. / Hsieh, F.L. / Gabelli, S.B. / Nathans, J.
Funding support United States, France, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY018637 United States
Howard Hughes Medical Institute (HHMI) United States
Human Frontier Science Program (HFSP)LT000130/2017-L France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure of the RECK CC domain, an evolutionary anomaly.
Authors: Chang, T.H. / Hsieh, F.L. / Smallwood, P.M. / Gabelli, S.B. / Nathans, J.
History
DepositionMar 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 18, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein,Reversion-inducing cysteine-rich protein with Kazal motifs fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7586
Polymers49,0961
Non-polymers6615
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.404, 110.221, 57.816
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltodextrin-binding protein,Reversion-inducing cysteine-rich protein with Kazal motifs fusion / mRECK


Mass: 49096.473 Da / Num. of mol.: 1
Mutation: D84A,K85A,E174A,N175A,A217H,K221H,K241A,A314V,I319V,E361A,K364A,D365A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Mus musculus (house mouse)
Gene: malE, DJ492_13065, EPS91_05465, FV295_14110, NCTC8450_00456, Reck
Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle (DE3)
References: UniProt: A0A376KDN7, UniProt: Q9Z0J1, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 508 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.86 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, 25% PEG 4000

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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: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.65→64.85 Å / Num. obs: 62274 / % possible obs: 100 % / Redundancy: 22.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.049 / Rrim(I) all: 0.235 / Net I/σ(I): 7.9 / Num. measured all: 1420849 / Scaling rejects: 2972
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
1.65-1.6917.80.22078027545070.630.5282.2721.999.5
7.38-64.8522.40.101181238090.9970.0220.10312.2100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.32 Å64.96 Å
Translation6.32 Å64.96 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.3data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SET

3set


Resolution: 1.651→57.816 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1774 3043 5.05 %
Rwork0.1559 59058 -
obs0.157 62202 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.69 Å2 / Biso mean: 28.4336 Å2 / Biso min: 10.06 Å2
Refinement stepCycle: final / Resolution: 1.651→57.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 65 507 3900
Biso mean--26.39 36.99 -
Num. residues----432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.651-1.67670.29411320.272242891
1.6767-1.70420.27591470.2512653100
1.7042-1.73360.23351210.23292630100
1.7336-1.76510.23431420.21392690100
1.7651-1.7990.23281430.19482665100
1.799-1.83580.2121360.17372664100
1.8358-1.87570.21051430.17082666100
1.8757-1.91930.18911460.16372656100
1.9193-1.96730.16571460.15542663100
1.9673-2.02050.18981590.15512651100
2.0205-2.080.18241400.15522688100
2.08-2.14710.20261590.15232657100
2.1471-2.22380.15371410.14012684100
2.2238-2.31290.17551460.14152714100
2.3129-2.41820.17161490.13562675100
2.4182-2.54560.16341270.13852686100
2.5456-2.70510.1511460.13712705100
2.7051-2.9140.19211460.14862720100
2.914-3.20720.17851380.1572733100
3.2072-3.67130.16171440.14942739100
3.6713-4.62510.14691560.13392757100
4.6251-57.8160.18191370.17432934100
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)
10.60550.1301-0.11510.5489-0.26740.60010.09660.10060.1772-0.114-0.0650.1342-0.098-0.13540.0080.16210.02980.0150.14080.01890.1876-10.022140.9681-18.994
20.428-0.1031-0.14550.46890.00380.41670.0228-0.0365-0.0654-0.0009-0.0439-0.04890.01750.07460.02380.1020.01260.0120.13410.01810.0968-4.572222.4489-9.8279
30.6221-0.0293-0.38330.71390.13050.88270.04620.0024-0.069-0.005-0.06480.02160.0304-0.02380.0040.07020.02020.00470.07680.00050.0869-10.514614.9951-12.3136
40.66260.1454-0.1310.33860.04480.27760.0554-0.06330.04890.0175-0.0465-0.0638-0.03410.0863-0.00010.120.00530.01460.11430.01410.1113-0.694830.8533-9.7014
50.0083-0.049-0.20560.1132-0.15270.0525-0.05080.12770.011-0.29710.0770.14410.10360.05220.05370.21660.0053-0.01990.2266-0.0260.1444-6.755620.8192-31.8588
60.1998-0.09860.18290.2489-0.17310.29350.0489-0.20520.06090.0781-0.0795-0.018-0.0753-0.058500.1831-0.00870.01510.2486-0.04390.15421.310940.3196-47.7526
72.37051.5863-0.47112.54491.50412.3777-0.4032-1.90562.75773.5850.3836-4.3829-0.23292.65080.030.96610.0055-0.07880.9421-0.17170.86114.53630.8359-46.9195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 74 )A4 - 74
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 155 )A75 - 155
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 247 )A156 - 247
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 335 )A248 - 335
5X-RAY DIFFRACTION5chain 'A' and (resid 336 through 389 )A336 - 389
6X-RAY DIFFRACTION6chain 'A' and (resid 390 through 434 )A390 - 434
7X-RAY DIFFRACTION7chain 'A' and (resid 435 through 435 )A435

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