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- PDB-3b2z: Crystal Structure of ADAMTS4 (apo form) -

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Basic information

Entry
Database: PDB / ID: 3b2z
TitleCrystal Structure of ADAMTS4 (apo form)
ComponentsADAMTS-4
KeywordsHYDROLASE / metalloprotease / aggrecanase / Cleavage on pair of basic residues / Extracellular matrix / Glycoprotein / Metal-binding / Secreted / Zymogen
Function / homology
Function and homology information


ADAMTS-4 endopeptidase / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / proteoglycan catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / skeletal system development / metalloendopeptidase activity ...ADAMTS-4 endopeptidase / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / proteoglycan catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / skeletal system development / metalloendopeptidase activity / metallopeptidase activity / peptidase activity / : / protease binding / defense response to bacterium / nuclear speck / proteolysis / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
YefM-like fold - #60 / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / : / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain / YefM-like fold ...YefM-like fold - #60 / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / : / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain / YefM-like fold / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
A disintegrin and metalloproteinase with thrombospondin motifs 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMosyak, L. / Stahl, M. / Somers, W.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structures of the two major aggrecan degrading enzymes, ADAMTS4 and ADAMTS5.
Authors: Mosyak, L. / Georgiadis, K. / Shane, T. / Svenson, K. / Hebert, T. / McDonagh, T. / Mackie, S. / Olland, S. / Lin, L. / Zhong, X. / Kriz, R. / Reifenberg, E.L. / Collins-Racie, L.A. / ...Authors: Mosyak, L. / Georgiadis, K. / Shane, T. / Svenson, K. / Hebert, T. / McDonagh, T. / Mackie, S. / Olland, S. / Lin, L. / Zhong, X. / Kriz, R. / Reifenberg, E.L. / Collins-Racie, L.A. / Corcoran, C. / Freeman, B. / Zollner, R. / Marvell, T. / Vera, M. / Sum, P.E. / Lavallie, E.R. / Stahl, M. / Somers, W.
History
DepositionOct 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADAMTS-4
B: ADAMTS-4
C: ADAMTS-4
D: ADAMTS-4
E: ADAMTS-4
F: ADAMTS-4
G: ADAMTS-4
H: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,93832
Polymers273,7738
Non-polymers1,16524
Water5,386299
1
A: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3674
Polymers34,2221
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3674
Polymers34,2221
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3674
Polymers34,2221
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3674
Polymers34,2221
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3674
Polymers34,2221
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3674
Polymers34,2221
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3674
Polymers34,2221
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: ADAMTS-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3674
Polymers34,2221
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.330, 84.315, 150.146
Angle α, β, γ (deg.)90.00, 112.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ADAMTS-4 / A disintegrin and metalloproteinase with thrombospondin motifs 4 / ADAM-TS 4 / ADAM-TS4 / ...A disintegrin and metalloproteinase with thrombospondin motifs 4 / ADAM-TS 4 / ADAM-TS4 / Aggrecanase-1 / ADMP-1


Mass: 34221.660 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS4, KIAA0688 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O75173, ADAMTS-4 endopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 72528 / Observed criterion σ(F): 0 / Rsym value: 0.12 / Net I/σ(I): 5.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rjp

2rjp


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.879 / SU B: 47.322 / SU ML: 0.416 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.312 3658 5 %RANDOM
Rwork0.254 ---
obs0.257 72512 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.852 Å2
Baniso -1Baniso -2Baniso -3
1--4.59 Å20 Å2-0.86 Å2
2--8.05 Å20 Å2
3----4.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17286 0 24 299 17609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02117829
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.95224354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09652283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86323.625742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.361152627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.70915104
X-RAY DIFFRACTIONr_chiral_restr0.0790.22671
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213798
X-RAY DIFFRACTIONr_nbd_refined0.2340.28488
X-RAY DIFFRACTIONr_nbtor_refined0.3030.211899
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2719
X-RAY DIFFRACTIONr_metal_ion_refined0.1220.245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.210
X-RAY DIFFRACTIONr_mcbond_it0.3291.511713
X-RAY DIFFRACTIONr_mcangle_it0.59218514
X-RAY DIFFRACTIONr_scbond_it0.77136739
X-RAY DIFFRACTIONr_scangle_it1.2614.55840
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 254 -
Rwork0.362 5012 -
all-5266 -
obs--97.75 %
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)
14.34420.4411-0.73820.69230.36034.90120.00310.2115-0.1330.09550.02250.060.10510.4749-0.0257-0.30920.05150.0063-0.35170.0175-0.246242.021-13.91898.251
26.96720.0145-0.95111.432-1.39243.62930.1590.3470.23050.0421-0.03940.0576-0.06550.4793-0.1197-0.2959-0.0598-0.05740.1023-0.0373-0.084221.944-13.4963.651
33.4684-0.2711-0.66650.8184-0.44734.516-0.0283-0.0063-0.0887-0.07340.0039-0.04310.0194-0.33350.0244-0.3364-0.0598-0.0137-0.0705-0.1119-0.201-21.541-13.73390.116
45.78620.6874-1.20971.36580.95673.97440.1008-0.37580.0125-0.0532-0.0569-0.035-0.1521-0.5532-0.0439-0.25790.1215-0.0362-0.37810.0647-0.0759-1.321-13.587124.577
54.5488-0.0511-1.11850.5476-0.75797.85980.0509-0.3266-0.0686-0.0448-0.0491-0.00140.3615-0.5434-0.0018-0.1192-0.06930.0067-0.6307-0.045-0.141831.689-13.68150.97
66.42260.3458-1.1761.46930.41356.3518-0.18850.5655-0.1029-0.09770.10730.0454-0.28960.1210.0813-0.2359-0.0116-0.04970.0929-0.01-0.182375.372-11.10361.549
77.3901-0.3727-1.16991.076-0.0425.9319-0.2179-0.6514-0.24770.12870.0635-0.1271-0.16820.38640.1544-0.2572-0.03530.0012-0.273-0.034-0.2046-55.12-11.67126.752
83.32680.1299-1.15760.51780.825413.4072-0.0741-0.1692-0.01230.0036-0.14750.00760.68651.82350.2216-0.15880.1239-0.01490.01860.0727-0.1452-11.338-14.59937.124
90.00150.00570.00830.02160.03240.07250.00880.1248-0.0113-0.00310.00060.0193-0.0082-0.0197-0.00940.42420.0528-0.01570.19340.05160.48719.365-12.382393.7347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A215 - 429
2X-RAY DIFFRACTION1A430 - 507
3X-RAY DIFFRACTION2B216 - 429
4X-RAY DIFFRACTION2B430 - 507
5X-RAY DIFFRACTION3C215 - 429
6X-RAY DIFFRACTION3C430 - 507
7X-RAY DIFFRACTION4D216 - 429
8X-RAY DIFFRACTION4D430 - 507
9X-RAY DIFFRACTION5E218 - 429
10X-RAY DIFFRACTION5E430 - 509
11X-RAY DIFFRACTION6F215 - 429
12X-RAY DIFFRACTION6F430 - 507
13X-RAY DIFFRACTION7G215 - 429
14X-RAY DIFFRACTION7G430 - 507
15X-RAY DIFFRACTION8H217 - 429
16X-RAY DIFFRACTION8H430 - 508
17X-RAY DIFFRACTION9A510 - 560
18X-RAY DIFFRACTION9C510 - 545
19X-RAY DIFFRACTION9B510 - 546
20X-RAY DIFFRACTION9E510 - 530
21X-RAY DIFFRACTION9D510 - 572
22X-RAY DIFFRACTION9G510 - 537
23X-RAY DIFFRACTION9F510 - 535
24X-RAY DIFFRACTION9H510 - 545

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