PDB-9um3: CaPETaseM9 SEC loop of 6CLb variant

ID or keywords:

Entry

Database: PDB / ID: 9um3

Title

CaPETaseM9 SEC loop of 6CLb variant

Components

Cutinase

Keywords

HYDROLASE / PETase / Cryptosporangium / aurantiacum / CaPETase

Function / homology

Cutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / PET hydrolase/cutinase-like domain-containing protein

Function and homology information

Biological species

Cryptosporangium aurantiacum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 Å

Authors

Kim, K. / Ki, D. / Park, J.

Funding support

1items

Citation

Journal: To Be Published
Title: Mechanistic Insights into Modulation of Productive Substrate Accessibility for Efficient PET Depolymerization
Authors: Kim, K. / Ki, D. / Park, J.

History

Deposition	Apr 21, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9um3.cif.gz	203.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9um3.ent.gz	161.7 KB	Display	PDB format
PDBx/mmJSON format	9um3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/um/9um3 ftp://data.pdbj.org/pub/pdb/validation_reports/um/9um3	HTTPS FTP

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Related structure data

Related structure data	9um4C 9um5C 9um6C 9um8C 7ymeS S: Starting model for refinement 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: Cutinase

B: Cutinase

C: Cutinase

D: Cutinase

113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cutinase

defined by author&software
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cutinase

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

3

C: Cutinase

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

4

D: Cutinase

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

Unit cell

Length a, b, c (Å)	139.039, 83.691, 79.020
Angle α, β, γ (deg.)	90.00, 90.65, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Cutinase Mass: 28287.678 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: CaPETaseM9 SEC loop of 6CLb variant Source: (gene. exp.) Cryptosporangium aurantiacum (bacteria) Gene: SAMN05443668_101498 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M7II12
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG 8000, 100 mM Tris base/ Hydrochloric acid pH 8.5, 200mM Magnesium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 24, 2023

Radiation

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

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 60096 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC_1/2: 0.984 / CC star: 0.996 / R_merge(I) obs: 0.098 / R_pim(I) all: 0.06 / R_rim(I) all: 0.115 / Χ²: 5.682 / Net I/σ(I): 14.5 / Num. measured all: 222149

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2-2.03	3.7	0.329	2992	0.927	0.981	0.199	0.386	3.083	99.7
2.03-2.07	3.7	0.303	3047	0.93	0.982	0.183	0.355	3.213	99.8
2.07-2.11	3.7	0.271	2940	0.935	0.983	0.164	0.317	3.513	99.9
2.11-2.15	3.7	0.251	2987	0.949	0.987	0.152	0.294	3.819	99.9
2.15-2.2	3.7	0.226	3045	0.96	0.99	0.136	0.264	4.14	99.9
2.2-2.25	3.7	0.208	3002	0.964	0.991	0.125	0.243	4.236	99.9
2.25-2.31	3.7	0.196	2993	0.965	0.991	0.118	0.23	4.259	99.9
2.31-2.37	3.7	0.179	3000	0.968	0.992	0.107	0.209	4.492	100
2.37-2.44	3.7	0.17	2994	0.969	0.992	0.102	0.198	4.738	100
2.44-2.52	3.7	0.156	3012	0.976	0.994	0.094	0.182	4.99	100
2.52-2.61	3.7	0.142	3014	0.977	0.994	0.085	0.166	5.361	100
2.61-2.71	3.7	0.13	2992	0.979	0.995	0.078	0.152	5.454	100
2.71-2.84	3.7	0.118	3007	0.982	0.996	0.071	0.137	5.961	100
2.84-2.99	3.7	0.111	3016	0.981	0.995	0.067	0.13	6.2	100
2.99-3.17	3.7	0.1	3009	0.985	0.996	0.06	0.116	7.419	100
3.17-3.42	3.7	0.09	3018	0.987	0.997	0.054	0.105	8.48	100
3.42-3.76	3.7	0.083	3037	0.989	0.997	0.05	0.097	9.872	99.9
3.76-4.31	3.7	0.073	3011	0.989	0.997	0.045	0.086	10.105	99.3
4.31-5.43	3.6	0.068	3023	0.989	0.997	0.042	0.08	8.154	99
5.43-50	3.3	0.063	2957	0.989	0.997	0.041	0.075	6.41	95.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-2000		data scaling
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7YME

7yme

Resolution: 2.01→28.74 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.941 / SU B: 4.695 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21901	3089	5.1 %	RANDOM
R_work	0.17543	-	-	-
obs	0.17778	57000	98.89 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.969 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.14 Å²	0 Å²	2.02 Å²
2-	-	-3.02 Å²	0 Å²
3-	-	-	-1.17 Å²

Refinement step

Cycle: 1 / Resolution: 2.01→28.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7759	0	0	208	7967

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	7986
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7234
X-RAY DIFFRACTION	r_angle_refined_deg	1.63	1.781	10931
X-RAY DIFFRACTION	r_angle_other_deg	0.551	1.736	16619
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.844	5	1014
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.868	5	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.971	10	1117
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	1188
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	9776
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1964
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.614	3.024	4068
X-RAY DIFFRACTION	r_mcbond_other	2.614	3.024	4068
X-RAY DIFFRACTION	r_mcangle_it	3.547	5.425	5078
X-RAY DIFFRACTION	r_mcangle_other	3.547	5.426	5079
X-RAY DIFFRACTION	r_scbond_it	3.308	3.327	3918
X-RAY DIFFRACTION	r_scbond_other	3.308	3.328	3919
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.842	5.978	5854
X-RAY DIFFRACTION	r_long_range_B_refined	6.107	30.03	8827
X-RAY DIFFRACTION	r_long_range_B_other	6.094	29.83	8816
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.01→2.058 Å

	R_factor	Num. reflection	% reflection
R_free	0.277	178	-
R_work	0.231	3879	-
obs	-	-	90.22 %

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