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- PDB-1rtg: C-TERMINAL DOMAIN (HAEMOPEXIN-LIKE DOMAIN) OF HUMAN MATRIX METALL... -

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Basic information

Entry
Database: PDB / ID: 1rtg
TitleC-TERMINAL DOMAIN (HAEMOPEXIN-LIKE DOMAIN) OF HUMAN MATRIX METALLOPROTEINASE-2
ComponentsHUMAN GELATINASE A
KeywordsMETALLOPROTEASE / MATRIX METALLO PROTEINASE (MMP) / GELATINASE / METZINCINS
Function / homology
Function and homology information


gelatinase A / intramembranous ossification / peripheral nervous system axon regeneration / blood vessel maturation / luteinization / parturition / bone trabecula formation / trophoblast cell migration / tissue remodeling / cellular response to UV-A ...gelatinase A / intramembranous ossification / peripheral nervous system axon regeneration / blood vessel maturation / luteinization / parturition / bone trabecula formation / trophoblast cell migration / tissue remodeling / cellular response to UV-A / ovulation from ovarian follicle / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / prostate gland epithelium morphogenesis / negative regulation of cell adhesion / cellular response to fluid shear stress / face morphogenesis / negative regulation of vasoconstriction / Activation of Matrix Metalloproteinases / macrophage chemotaxis / endodermal cell differentiation / response to amyloid-beta / Collagen degradation / collagen catabolic process / fibronectin binding / extracellular matrix disassembly / response to electrical stimulus / EPH-ephrin mediated repulsion of cells / cellular response to interleukin-1 / response to hyperoxia / ephrin receptor signaling pathway / response to retinoic acid / response to mechanical stimulus / ovarian follicle development / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / extracellular matrix organization / sarcomere / response to activity / cellular response to reactive oxygen species / response to nicotine / cellular response to amino acid stimulus / cellular response to estradiol stimulus / response to hydrogen peroxide / protein catabolic process / metalloendopeptidase activity / response to estrogen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / cell migration / : / heart development / angiogenesis / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / response to hypoxia / Extra-nuclear estrogen signaling / positive regulation of cell migration / response to xenobiotic stimulus / serine-type endopeptidase activity / mitochondrion / proteolysis / extracellular space / extracellular region / zinc ion binding / nucleus / plasma membrane
Similarity search - Function
4 Propeller / Hemopexin / Hemopexin-like domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site ...4 Propeller / Hemopexin / Hemopexin-like domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / 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 / Metallopeptidase, catalytic domain superfamily / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature. / Mainly Beta
Similarity search - Domain/homology
72 kDa type IV collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsGohlke, U. / Bode, W.
Citation
Journal: FEBS Lett. / Year: 1996
Title: The C-terminal (haemopexin-like) domain structure of human gelatinase A (MMP2): structural implications for its function.
Authors: Gohlke, U. / Gomis-Ruth, F.X. / Crabbe, T. / Murphy, G. / Docherty, A.J. / Bode, W.
#1: Journal: Structure / Year: 1995
Title: A Helping Hand for Collagenases: The Haemopexin-Like Domain
Authors: Bode, W.
#2: Journal: Structure / Year: 1995
Title: Structure of Full-Length Porcine Synovial Collagenase Reveals a C-Terminal Domain Containing a Calcium-Linked, Four-Bladed Beta-Propeller
Authors: Li, J. / Brick, P. / O'Hare, M.C. / Skarzynski, T. / Lloyd, L.F. / Curry, V.A. / Clark, I.M. / Bigg, H.F. / Hazleman, B.L. / Cawston, T.E. / al., et
History
DepositionDec 21, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN GELATINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9424
Polymers23,8261
Non-polymers1163
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.780, 58.850, 93.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHERE IS ONE OLIGOTRIMER PRESENT IN THE ASYMMETRIC UNIT, I.E., ONE PROCARBOXYPEPTIDASE A MOLECULE, ONE PRO-PROTEINASE E MOLECULE, AND ONE CHYMOTRYPSINOGEN.

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Components

#1: Protein HUMAN GELATINASE A / HUMAN MATRIX METALLOPROTEINASE-2 / MMP-2


Mass: 23826.221 Da / Num. of mol.: 1
Fragment: C-TERMINAL RESIDUES 451 - 660, HAEMOPEXIN-LIKE DOMAIN
Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08253, gelatinase A
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.15 Mcitrate1drop
22.5 %PEG60001drop
30.9 Mcitrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 9618 / % possible obs: 96.7 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 9999 Å / Num. measured all: 34708
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.65 Å / % possible obs: 71.3 % / Rmerge(I) obs: 0.274

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Processing

Software
NameClassification
MOSFLM/CCP4data collection
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data reduction
X-PLORphasing
RefinementResolution: 2.6→8 Å /
RfactorNum. reflection
Rwork0.179 -
obs0.179 8574
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 1 73 1716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.1 Å2

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