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- PDB-1su3: X-ray structure of human proMMP-1: New insights into collagenase ... -

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Basic information

Entry
Database: PDB / ID: 1su3
TitleX-ray structure of human proMMP-1: New insights into collagenase action
ComponentsInterstitial collagenase
KeywordsHYDROLASE / Prodomain / Hemopexin domain / exocite / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / extracellular matrix / Degradation of the extracellular matrix ...interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
4 Propeller / Hemopexin / Hemopexin-like domain / 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 ...4 Propeller / Hemopexin / Hemopexin-like domain / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Interstitial collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJozic, D. / Bourenkov, G. / Lim, N.H. / Nagase, H. / Bode, W. / Maskos, K. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: X-ray structure of human proMMP-1: new insights into procollagenase activation and collagen binding.
Authors: Jozic, D. / Bourenkov, G. / Lim, N.H. / Visse, R. / Nagase, H. / Bode, W. / Maskos, K.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interstitial collagenase
B: Interstitial collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24224
Polymers103,8242
Non-polymers1,41822
Water6,702372
1
A: Interstitial collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,35810
Polymers51,9121
Non-polymers4469
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interstitial collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,88414
Polymers51,9121
Non-polymers97213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Interstitial collagenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)423,074112
Polymers415,2978
Non-polymers7,777104
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_545x,-y-1,-z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area23050 Å2
ΔGint-910 kcal/mol
Surface area141570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.746, 142.746, 295.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Interstitial collagenase / / Matrix metalloproteinase-1 / MMP-1 / Fibroblast collagenase


Mass: 51912.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP1, CLG / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03956, interstitial collagenase

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Non-polymers , 7 types, 394 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.62 Å3/Da / Density % sol: 66.04 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5M Li2SO4, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.28200, 1.28380, 1.0500
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2821
21.28381
31.051
ReflectionResolution: 2.02→20 Å / Num. obs: 72595 / Redundancy: 5.46 % / Rsym value: 0.07 / Net I/σ(I): 27.26
Reflection shellHighest resolution: 2.02 Å / Redundancy: 5.46 % / Mean I/σ(I) obs: 27.26 / Rsym value: 0.07

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.229 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25233 3885 5.1 %RANDOM
Rwork0.22269 ---
obs0.22422 72595 100 %-
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: 39.405 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6674 0 53 372 7099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216899
X-RAY DIFFRACTIONr_bond_other_d0.0020.025878
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9349358
X-RAY DIFFRACTIONr_angle_other_deg0.789313702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3765823
X-RAY DIFFRACTIONr_chiral_restr0.0840.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027751
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021530
X-RAY DIFFRACTIONr_nbd_refined0.2110.21407
X-RAY DIFFRACTIONr_nbd_other0.2350.26975
X-RAY DIFFRACTIONr_nbtor_other0.0870.23924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2316
X-RAY DIFFRACTIONr_metal_ion_refined0.150.245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4250.222
X-RAY DIFFRACTIONr_mcbond_it0.7361.54121
X-RAY DIFFRACTIONr_mcangle_it1.35726612
X-RAY DIFFRACTIONr_scbond_it1.85432778
X-RAY DIFFRACTIONr_scangle_it3.0254.52746
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.25 299
Rwork0.226 5241
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)
10.0052-0.08470.04410.1880.16660.0539-0.06580.03610.01750.07450.0998-0.23030.09760.123-0.0340.257000.25700.25757.429-28.87257.066
20.0472-0.01280.13680.89830.99260.4993-0.02790.05440.0459-0.0593-0.09940.01210.136-0.1540.12730.2114-0.06090.04560.1529-0.01960.135139.844-33.96652.096
30.13960.02560.11881.93270.43590.3126-0.01410.04840.14240.2927-0.068-0.1386-0.0926-0.0730.08210.2060.05050.11990.07370.09010.129840.864-0.90353.246
46.6562-1.16450.9226-0.91070.9802-0.20750.10810.37440.0261-0.239-0.17540.53150.2237-0.34950.06730.2571-0.000100.25700.2579.553-88.13613.935
52.1001-0.71180.04721.3519-0.57681.6062-0.02910.07070.0127-0.1193-0.0814-0.0030.05620.07070.11040.14940.00740.03470.11610.00030.078632.404-92.91315.819
61.43980.5013-0.07422.03840.53351.1872-0.007-0.13140.1157-0.0592-0.08160.31990.0018-0.00910.08860.12220.00550.01960.1347-0.0640.104123.115-57.30323.615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA32 - 9813 - 79
2X-RAY DIFFRACTION2AA107 - 27088 - 251
3X-RAY DIFFRACTION3AA271 - 465252 - 446
4X-RAY DIFFRACTION4BB32 - 9813 - 79
5X-RAY DIFFRACTION5BB107 - 27088 - 251
6X-RAY DIFFRACTION6BB271 - 465252 - 446

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