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- PDB-4u7k: Crystal structure of the Clostridium histolyticum colH collagenas... -

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Basic information

Entry
Database: PDB / ID: 4u7k
TitleCrystal structure of the Clostridium histolyticum colH collagenase polycystic kidney disease-like domain 2a in the presence of calcium at 1.9 Angstrom resolution
ComponentsColH protein
KeywordsHYDROLASE / Calcium-binding protein
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
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. ...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. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium histolyticum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.91 Å
AuthorsBauer, R. / Janowska, K. / Sakon, J. / Matsushita, O. / Latimer, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103429 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH.
Authors: Bauer, R. / Janowska, K. / Taylor, K. / Jordan, B. / Gann, S. / Janowski, T. / Latimer, E.C. / Matsushita, O. / Sakon, J.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 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 / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ColH protein
B: ColH protein
C: ColH protein
D: ColH protein
E: ColH protein
F: ColH protein
G: ColH protein
H: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,62016
Polymers77,2998
Non-polymers3218
Water17,421967
1
A: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7032
Polymers9,6621
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7032
Polymers9,6621
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7032
Polymers9,6621
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7032
Polymers9,6621
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7032
Polymers9,6621
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7032
Polymers9,6621
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7032
Polymers9,6621
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: ColH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7032
Polymers9,6621
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.320, 87.610, 104.350
Angle α, β, γ (deg.)90.000, 116.040, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 3 / Auth seq-ID: 685 - 770 / Label seq-ID: 2 - 87

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

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Components

#1: Protein
ColH protein / Collagenase


Mass: 9662.437 Da / Num. of mol.: 8
Fragment: polycystic kidney disease-like domain (UNP residues 724-810)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium histolyticum (bacteria) / Gene: colH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q46085
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl pH 8.5, and 30% (w/v) PEG 4000. Crystals soaked in 0.2 M magnesium chloride, 0.05 M calcium chloride, 0.1 M Tris-HCl pH 8.5, and 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 14, 2013 / Details: CCD
RadiationMonochromator: Osmic Blue confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.91→22.11 Å / Num. obs: 61851 / % possible obs: 96.4 % / Redundancy: 3.63 % / Rmerge(I) obs: 0.046 / Χ2: 1.14 / Net I/σ(I): 13.8 / Num. measured all: 226167 / Scaling rejects: 1697
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.91-1.983.110.3131891260091.5719893.8
1.98-2.063.240.224.21957760091.3510594.2
2.06-2.153.510.1765.72142460651.2812695
2.15-2.263.760.1527.12315361031.2618695.4
2.26-2.413.80.11982356661781.138396.2
2.41-2.593.810.09210.22360161741.097196.6
2.59-2.853.770.07113.42366662191.119697.3
2.85-3.263.810.04919.52405362910.9610697.9
3.26-4.113.740.03427.62394863320.8829498.4
4.11-22.113.70.026342426764710.9433298.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
d*TREK9.9.9.4 W9RSSIdata reduction
PDB_EXTRACT3.14data extraction
d*TREKdata scaling
RefinementResolution: 1.91→93.76 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.675 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 3119 5 %RANDOM
Rwork0.1629 58720 --
obs0.1651 61839 96.28 %-
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 max: 90.38 Å2 / Biso mean: 33.81 Å2 / Biso min: 16.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.48 Å2
2--0.63 Å20 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 1.91→93.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5368 0 8 967 6343
Biso mean--28.24 46.18 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225488
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9597377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.84226.875256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.118151007
X-RAY DIFFRACTIONr_chiral_restr0.10.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0214136
X-RAY DIFFRACTIONr_mcbond_it2.6561.53384
X-RAY DIFFRACTIONr_mcangle_it3.9325480
X-RAY DIFFRACTIONr_scbond_it6.77132104
X-RAY DIFFRACTIONr_scangle_it11.2274.51897
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A344TIGHT POSITIONAL0.080.05
2B344TIGHT POSITIONAL0.070.05
3C344TIGHT POSITIONAL0.080.05
4D344TIGHT POSITIONAL0.090.05
5E344TIGHT POSITIONAL0.070.05
6F344TIGHT POSITIONAL0.080.05
7G344TIGHT POSITIONAL0.060.05
8H344TIGHT POSITIONAL0.050.05
1A321LOOSE POSITIONAL0.15
2B321LOOSE POSITIONAL0.095
3C321LOOSE POSITIONAL0.15
4D321LOOSE POSITIONAL0.195
5E321LOOSE POSITIONAL0.15
6F321LOOSE POSITIONAL0.15
7G321LOOSE POSITIONAL0.085
8H321LOOSE POSITIONAL0.085
1A344TIGHT THERMAL0.760.5
2B344TIGHT THERMAL0.680.5
3C344TIGHT THERMAL0.690.5
4D344TIGHT THERMAL0.660.5
5E344TIGHT THERMAL0.660.5
6F344TIGHT THERMAL0.640.5
7G344TIGHT THERMAL0.650.5
8H344TIGHT THERMAL0.690.5
1A321LOOSE THERMAL0.7210
2B321LOOSE THERMAL0.6510
3C321LOOSE THERMAL0.6710
4D321LOOSE THERMAL0.5810
5E321LOOSE THERMAL0.6510
6F321LOOSE THERMAL0.6510
7G321LOOSE THERMAL0.6410
8H321LOOSE THERMAL0.610
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 244 -
Rwork0.255 4175 -
all-4419 -
obs--93.54 %
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)
11.6614-1.17880.98273.756-0.74532.1076-0.04970.09940.0391-0.19370.02360.2162-0.1360.06620.0260.035-0.0132-0.0020.00580.01080.04871.0539-18.889738.0642
25.2264-1.6535-0.67571.52010.16981.7021-0.0779-0.45990.10380.00680.0741-0.1169-0.14770.39960.00370.0187-0.030.0110.1195-0.00820.037222.029-24.575260.7051
31.8678-0.9964-1.51132.11032.38694.7978-0.0434-0.3908-0.04580.2220.10820.01930.30720.1308-0.06480.0403-0.00180.01630.09670.00890.0326.2734-30.830770.6354
41.25440.03360.70862.06180.45232.55290.138-0.0175-0.1258-0.21140.04970.050.2695-0.1508-0.18760.0773-0.02-0.01680.00860.01280.0526-5.4355-36.895941.6152
53.1351-0.42240.6130.9931-0.03082.0738-0.03880.0238-0.0542-0.0067-0.0038-0.0339-0.07650.35790.04260.0129-0.01120.01910.06370.01240.0325-6.6722-22.411413.9622
62.4208-0.5405-0.93351.20750.69424.26080.0896-0.3565-0.02040.07220.0058-0.01630.05470.0038-0.09530.0146-0.02330.00760.05680.00430.0259-21.7814-29.878123.6887
72.00661.42220.79713.81310.53691.2555-0.0108-0.15440.07410.4266-0.0091-0.1884-0.1151-0.09230.01990.11150.0139-0.01680.0153-0.02060.0527.6385-17.12178.5032
81.2381.382-0.90155.4562-3.70414.71850.1055-0.0519-0.19450.4457-0.2313-0.3801-0.00260.31350.12570.08760.0003-0.040.01550.00910.063132.902-35.56645.3723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A685 - 770
2X-RAY DIFFRACTION2B685 - 770
3X-RAY DIFFRACTION3C685 - 770
4X-RAY DIFFRACTION4D685 - 770
5X-RAY DIFFRACTION5E685 - 770
6X-RAY DIFFRACTION6F685 - 770
7X-RAY DIFFRACTION7G685 - 770
8X-RAY DIFFRACTION8H685 - 770

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