PDB-9p16: Thermolysin Room-Temperature In-Situ, Grown On-Site

ID or keywords:

Entry

Database: PDB / ID: 9p16

Title

Thermolysin Room-Temperature In-Situ, Grown On-Site

Components

Thermolysin

Keywords

HYDROLASE / thermostable / metalloprotease

Function / homology

Function and homology information

thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function

Biological species

Geobacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Campomizzi, C.S. / Snell, M.E. / Mikolajek, H. / Sandy, J. / Sanchez-Weatherby, J. / Budziszewski, G.R. / Hough, M.A. / Bowman, S.E.J.

Funding support

United States, 1items

Citation

Journal: Biorxiv / Year: 2025
Title: Does crossing the pond affect crystal quality?
Authors: Campomizzi, C.S. / Snell, M.E. / Mikolajek, H. / Sandy, J. / Sanchez-Weatherby, J. / Budziszewski, G.R. / Russi, S. / Howells Jr., R. / Cohen, A. / Hough, M.A. / Bowman, S.E.J.

History

Deposition	Jun 9, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 27, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9p16.cif.gz	135.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9p16.ent.gz	102.1 KB	Display	PDB format
PDBx/mmJSON format	9p16.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9p16_validation.pdf.gz	427.7 KB	Display	wwPDB validaton report
Full document	9p16_full_validation.pdf.gz	428 KB	Display
Data in XML	9p16_validation.xml.gz	17.2 KB	Display
Data in CIF	9p16_validation.cif.gz	24.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p1/9p16 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/9p16	HTTPS FTP

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Related structure data

Related structure data	9p12C 9p13C 9p14C 9p15C 9p17C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thermolysin

hetero molecules

34.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	93.073, 93.073, 130.561
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-711- HOH

#1: Protein	Thermolysin / Neutral protease Mass: 34360.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: nprS, nprM / Production host: Geobacillus stearothermophilus (bacteria) / References: UniProt: P43133, thermolysin
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.20 M sodium di-hydrogen phosphate, 16.7% polyethylene glycol (PEG) 3350

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Data collection

Diffraction

Mean temperature: 293 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: VMXi / Wavelength: 0.7749 Å

Detector

Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Oct 3, 2024

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.7749 Å / Relative weight: 1

Reflection

Resolution: 1.73→80.6 Å / Num. obs: 35537 / % possible obs: 100 % / Redundancy: 11.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.181 / R_pim(I) all: 0.077 / R_rim(I) all: 0.197 / Χ²: 0.96 / Net I/σ(I): 9.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
8.99-80.6	10	0.029	41.3	322	1	0.012	0.031	0.49	99.9
1.73-1.76	5.7	1.95	0.8	1925	0.288	1.292	2.352	0.93	100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
Aimless		data scaling
Coot		model building
xia2.multiplex		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.73→80.6 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.968 / SU B: 2.257 / SU ML: 0.066 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1726	1844	5.197 %
R_work	0.1469	33641	-
all	0.148	-	-
obs	-	35485	99.972 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.431 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.144 Å²	-0.072 Å²	-0 Å²
2-	-	-0.144 Å²	-0 Å²
3-	-	-	0.468 Å²

Refinement step

Cycle: LAST / Resolution: 1.73→80.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2412	0	10	212	2634

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	2505
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2170
X-RAY DIFFRACTION	r_angle_refined_deg	1.757	1.771	3420
X-RAY DIFFRACTION	r_angle_other_deg	0.627	1.735	4978
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.887	5	322
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.471	5	10
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.157	10	348
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.891	10	122
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	366
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3078
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	624
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	548
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	2039
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	1360
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1363
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	196
X-RAY DIFFRACTION	r_metal_ion_refined	0.115	0.2	22
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.271	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.205	0.2	47
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.442	0.2	41
X-RAY DIFFRACTION	r_mcbond_it	1.558	1.792	1282
X-RAY DIFFRACTION	r_mcbond_other	1.55	1.792	1282
X-RAY DIFFRACTION	r_mcangle_it	2.164	3.206	1606
X-RAY DIFFRACTION	r_mcangle_other	2.164	3.206	1607
X-RAY DIFFRACTION	r_scbond_it	2.925	2.106	1223
X-RAY DIFFRACTION	r_scbond_other	2.919	2.102	1218
X-RAY DIFFRACTION	r_scangle_it	4.458	3.703	1814
X-RAY DIFFRACTION	r_scangle_other	4.457	3.698	1809
X-RAY DIFFRACTION	r_lrange_it	13.043	27.164	3128
X-RAY DIFFRACTION	r_lrange_other	11.738	22.853	3071

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.73-1.775	0.322	129	0.31	2432	0.311	2562	0.921	0.919	99.961	0.311
1.775-1.824	0.279	140	0.278	2377	0.278	2519	0.937	0.942	99.9206	0.279
1.824-1.877	0.276	150	0.251	2269	0.253	2419	0.945	0.952	100	0.249
1.877-1.934	0.246	115	0.202	2267	0.204	2383	0.962	0.972	99.958	0.193
1.934-1.998	0.196	120	0.175	2173	0.176	2293	0.975	0.979	100	0.162
1.998-2.068	0.196	118	0.166	2129	0.168	2247	0.978	0.982	100	0.15
2.068-2.146	0.158	106	0.155	2043	0.155	2151	0.983	0.985	99.907	0.137
2.146-2.233	0.183	110	0.144	1973	0.146	2083	0.982	0.987	100	0.124
2.233-2.333	0.168	96	0.135	1910	0.137	2006	0.982	0.989	100	0.117
2.333-2.446	0.142	84	0.13	1833	0.131	1917	0.986	0.99	100	0.112
2.446-2.579	0.187	93	0.135	1737	0.137	1830	0.979	0.989	100	0.116
2.579-2.735	0.163	90	0.134	1650	0.135	1740	0.984	0.99	100	0.117
2.735-2.923	0.151	86	0.129	1556	0.13	1642	0.986	0.99	100	0.113
2.923-3.157	0.191	96	0.137	1430	0.14	1526	0.978	0.988	100	0.122
3.157-3.458	0.168	71	0.137	1352	0.138	1423	0.981	0.99	100	0.123
3.458-3.865	0.125	63	0.116	1238	0.116	1301	0.993	0.994	100	0.107
3.865-4.462	0.115	63	0.097	1099	0.098	1162	0.993	0.995	100	0.09
4.462-5.46	0.134	49	0.105	947	0.106	996	0.995	0.995	100	0.097
5.46-7.704	0.145	42	0.143	761	0.143	804	0.99	0.99	99.8756	0.133
7.704-80.6	0.142	23	0.136	465	0.137	491	0.994	0.987	99.389	0.128

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