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- PDB-1nqj: CRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLG COLLAGENASE CO... -

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Basic information

Entry
Database: PDB / ID: 1nqj
TitleCRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLG COLLAGENASE COLLAGEN-BINDING DOMAIN 3B AT 1.0 ANGSTROM RESOLUTION IN ABSENCE OF CALCIUM
Componentsclass 1 collagenase
KeywordsHYDROLASE / BETA SANDWICH / METALLOPROTEASE / COLLAGEN-BINDING DOMAIN / LITHIUM / CHLORINE
Function / homology
Function and homology information


tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
Jelly Rolls - #380 / Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / PKD domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain ...Jelly Rolls - #380 / Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / PKD domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Neutral zinc metallopeptidases, zinc-binding region signature. / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Collagenase ColG / Collagenase ColG
Similarity search - Component
Biological speciesClostridium histolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1 Å
AuthorsWilson, J.J. / Matsushita, O. / Okabe, A. / Sakon, J.
CitationJournal: Embo J. / Year: 2003
Title: A bacterial collagen-binding domain with novel calcium-binding motif controls domain orientation
Authors: Wilson, J.J. / Matsushita, O. / Okabe, A. / Sakon, J.
History
DepositionJan 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: class 1 collagenase
B: class 1 collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1077
Polymers27,0162
Non-polymers925
Water6,990388
1
A: class 1 collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5503
Polymers13,5081
Non-polymers422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: class 1 collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5574
Polymers13,5081
Non-polymers493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.637, 57.708, 46.320
Angle α, β, γ (deg.)90.00, 95.69, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

#1: Protein class 1 collagenase


Mass: 13507.840 Da / Num. of mol.: 2 / Fragment: COLLAGEN-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium histolyticum (bacteria) / Gene: ColG / Plasmid: pGEX-4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9S0X0, UniProt: Q9X721*PLUS, microbial collagenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Li
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 1.71 Å3/Da / Density % sol: 27.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 3350, LITHIUM CHLORIDE, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
122-25 %PEG33501reservoir
2100 mMsodium acetate1reservoirpH4.6
3600 mM1reservoirLiCl
410 %glycerol1reservoir
525000 ng/mlprotein1drop
60.2 mMEGTA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2000
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.983→36 Å / Num. all: 114718 / Num. obs: 105185 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.01 % / Rsym value: 0.075 / Net I/σ(I): 30.7
Reflection shellResolution: 1→1.07 Å / Mean I/σ(I) obs: 2.94 / Num. unique all: 15310 / Rsym value: 0.318 / % possible all: 72.64
Reflection
*PLUS
Highest resolution: 1 Å / Lowest resolution: 36 Å / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 72.64 %

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Processing

Software
NameClassification
SAINTdata scaling
SAINTdata reduction
SHELXmodel building
SHELXL-97refinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1→28.85 Å / Num. parameters: 20305 / Num. restraintsaints: 37831 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1677 10518 10 %RANDOM
Rwork0.1398 ---
all0.1416 86824 --
obs0.1416 86824 91.7 %-
Refine analyzeNum. disordered residues: 40 / Occupancy sum hydrogen: 1650 / Occupancy sum non hydrogen: 2066.53
Refinement stepCycle: LAST / Resolution: 1→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3717 0 5 388 4110
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0296
X-RAY DIFFRACTIONs_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.044
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0.06
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsTotal num. of bins used% reflection obs (%)
1-1.07X-RAY DIFFRACTION15310672.64
1.07-1.2X-RAY DIFFRACTION23987688.46
1.2-1.5X-RAY DIFFRACTION32076699.12
1.5-2X-RAY DIFFRACTION19604699.77
2-8X-RAY DIFFRACTION13990698.01
8-36X-RAY DIFFRACTION218688.62
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 28.9 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.166 / Rfactor Rwork: 0.142
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.03
X-RAY DIFFRACTIONs_chiral_restr0.082

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