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- PDB-3oho: catalytic domain of stromelysin-1 in complex with N-Hydroxy-2-(4-... -

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Basic information

Entry
Database: PDB / ID: 3oho
Titlecatalytic domain of stromelysin-1 in complex with N-Hydroxy-2-(4-methylphenylsulfonamido)acetamide
ComponentsStromelysin-1Matrix metalloproteinase
KeywordsHYDROLASE / Matrixmetalloproteinase
Function / homology
Function and homology information


stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / negative regulation of reactive oxygen species metabolic process / cellular response to nitric oxide ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / negative regulation of reactive oxygen species metabolic process / cellular response to nitric oxide / extracellular matrix disassembly / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell migration / EGFR Transactivation by Gastrin / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / protein catabolic process / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytosol
Similarity search - Function
Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin ...Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / 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
Chem-Z79 / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKowatz, T. / Naismith, J.H.
CitationJournal: To be Published
Title: Non-Resonance Raman Difference Spectroscopy as a Tool to Probe Enthalpy-Entropy Compensation and the Interfacial Mobility Model
Authors: Kowatz, T. / Naismith, J.H.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stromelysin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6108
Polymers19,0021
Non-polymers6077
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Stromelysin-1
hetero molecules

A: Stromelysin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,21916
Polymers38,0042
Non-polymers1,21514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2230 Å2
ΔGint-92 kcal/mol
Surface area15100 Å2
MethodPISA
3
A: Stromelysin-1
hetero molecules

A: Stromelysin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,21916
Polymers38,0042
Non-polymers1,21514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1500 Å2
ΔGint-57 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.482, 121.044, 46.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-267-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Stromelysin-1 / Matrix metalloproteinase / SL-1 / Matrix metalloproteinase-3 / MMP-3 / Transin-1


Mass: 19002.119 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN (UNP Residues 100-268)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP3, STMY1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3)Gold / References: UniProt: P08254, stromelysin 1

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Non-polymers , 5 types, 22 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-Z79 / N-hydroxy-N~2~-[(4-methoxyphenyl)sulfonyl]glycinamide


Mass: 260.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O5S
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M (NH4)2SO4, 0.1 M Na-cacodylate, pH 6.5, 26% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.5→25.6 Å / Num. obs: 5809 / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 26.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0079refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1b8y

1b8y


Resolution: 2.5→25.6 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.885 / SU B: 24.34 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26448 276 4.7 %RANDOM
Rwork0.25466 ---
obs0.25512 5540 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 94.18 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å2-0 Å20 Å2
2---2.12 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 27 15 1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221356
X-RAY DIFFRACTIONr_bond_other_d0.0010.02892
X-RAY DIFFRACTIONr_angle_refined_deg0.7821.9571818
X-RAY DIFFRACTIONr_angle_other_deg0.7573.0022144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2055156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02423.48566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44115190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.519157
X-RAY DIFFRACTIONr_chiral_restr0.0460.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02292
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 22 -
Rwork0.262 354 -
obs--90.6 %
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)
12.38520.5243-0.36929.92821.19243.28680.2031-0.1739-0.06491.5716-0.1389-1.07640.37010.3706-0.06420.4342-0.0174-0.14540.4050.09960.41878.683-15.2661.108
22.5982-0.4037-0.37076.33681.76595.78490.0167-0.1208-0.1690.5718-0.0015-0.6980.36480.2936-0.01520.28870.0037-0.03470.36970.040.36278.738-14.999-4.487
31.9609-3.297-2.52869.8252-0.20518.5845-0.1541-0.26050.71850.93370.1131-2.5348-0.03510.84220.0410.51240.0947-0.39470.53920.03161.193218.895-14.326-2.253
423.21062.1765-6.46697.4055-4.48673.9054-0.5568-1.69773.37871.0469-0.6418-3.5383-0.37960.86961.19862.33150.8299-1.92581.2547-0.58833.953223.424-17.384.52
50.32730.4248-0.06260.5613-0.09720.20670.03050.03890.24960.0450.01490.3967-0.16730.1356-0.04540.620.23840.18430.4081-0.01270.91568.17-19.563-17.109
60.11-0.1740.09470.3143-0.18650.1473-0.02160.00010.08560.0764-0.0611-0.17710.04530.1140.08270.5020.0497-0.0690.37850.01540.24953.223-9.072.317
70.15740.09610.04320.07880.05520.0613-0.00840.0120.1869-0.052700.0691-0.06340.00580.00840.3071-0.04990.08760.36630.02060.395813.443-11.305-16.684
80.0268-0.02420.00290.0230.00040.0089-0.00110.0030.0571-0.0068-0.0065-0.0475-0.0271-0.00790.00760.336-0.0234-0.02920.34250.0560.38696.808-7.637-8.573
90.06080.06680.01440.1988-0.00030.0418-0.0004-0.04070.0436-0.04460.02570.154-0.00990.1033-0.02520.315-0.0294-0.0590.53170.13790.860818.298-9.999-4.926
100.58110.2247-6.111946.62177.614466.47860.1314-0.0848-0.1071-0.2245-1.0807-0.6974-1.54330.76890.94930.0469-0.0618-0.0060.24030.02770.243918.2906-11.9922-8.2683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A83 - 116
2X-RAY DIFFRACTION2A117 - 192
3X-RAY DIFFRACTION3A193 - 220
4X-RAY DIFFRACTION4A221 - 249
5X-RAY DIFFRACTION5A1
6X-RAY DIFFRACTION6A2
7X-RAY DIFFRACTION7A3
8X-RAY DIFFRACTION8A4
9X-RAY DIFFRACTION9A5
10X-RAY DIFFRACTION10A252

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