PDB-7jos: Crystal structure of BbKI complexed with Human Kallikrein 4

ID or keywords:

Entry

Database: PDB / ID: 7jos

Title

Crystal structure of BbKI complexed with Human Kallikrein 4

Components

Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a
Kunitz-type inihibitor

Keywords

HYDROLASE/HYDROLASE INHIBITOR / inhibitor / PLANT PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

biomineral tissue development / amelogenesis / endopeptidase inhibitor activity / extracellular matrix disassembly / protein catabolic process / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function

Biological species

Homo sapiens (human)

Bauhinia bauhinioides (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Li, M. / Wlodawer, A. / Gustchina, A.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2021
Title: Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI
Authors: Li, M. / Srp, J. / Mares, M. / Wlodawer, A. / Gustchina, A.

History

Deposition	Aug 7, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 21, 2021	Provider: repository / Type: Initial release
Revision 1.1	Aug 11, 2021	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7jos.cif.gz	556 KB	Display	PDBx/mmCIF format
PDB format	pdb7jos.ent.gz	445.2 KB	Display	PDB format
PDBx/mmJSON format	7jos.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jo/7jos ftp://data.pdbj.org/pub/pdb/validation_reports/jo/7jos	HTTPS FTP

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Related structure data

Related structure data	7jodSC 7joeC 7jowC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7jos-6 7jr2-5 7jos-2 6dwu-11 7jqv-d 7jr1-1 1zm5-d 4j2y-d 7jos-4 7jos-5 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

7jodSC

7joeC

7jowC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

B: Kunitz-type inihibitor

C: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

D: Kunitz-type inihibitor

E: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

F: Kunitz-type inihibitor

G: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

H: Kunitz-type inihibitor

I: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

J: Kunitz-type inihibitor

K: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

L: Kunitz-type inihibitor

M: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

N: Kunitz-type inihibitor

294 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

B: Kunitz-type inihibitor

defined by author&software
Evidence: gel filtration
42.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

D: Kunitz-type inihibitor

defined by author&software
42.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

F: Kunitz-type inihibitor

defined by author&software
42.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

H: Kunitz-type inihibitor

defined by author&software
42.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

J: Kunitz-type inihibitor

defined by author&software
42.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

L: Kunitz-type inihibitor

defined by author&software
42.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

M: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a

N: Kunitz-type inihibitor

defined by author&software
42.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.143, 117.195, 159.417
Angle α, β, γ (deg.)	90.000, 89.571, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

#1: Protein	Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a / Kallikrein B1 / Kallikrein-4 Mass: 23926.010 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, KLNB1, hCG_1641510 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C4DFQ5
#2: Protein	Kunitz-type inihibitor Mass: 18140.520 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bauhinia bauhinioides (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VEQ7
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1339 / 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: 2.92 Å³/Da / Density % sol: 57.92 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 0.2M NaCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 192940 / % possible obs: 97.4 % / Redundancy: 3.4 % / R_sym value: 0.065 / Net I/σ(I): 15.93
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 1.9 % / Num. unique obs: 7985 / R_sym value: 1.057

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7jod

7jod

Resolution: 2.1→49.494 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.934 / SU B: 5.175 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / ESU R: 0.213 / ESU R Free: 0.17
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2122	1650	0.968 %
R_work	0.1839	168772	-
all	0.184	-	-
obs	-	170422	86.387 %

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: 33.785 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.208 Å²	0 Å²	-0.087 Å²
2-	-	-0.28 Å²	-0 Å²
3-	-	-	0.071 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→49.494 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20629	0	0	1339	21968

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	21254
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	19305
X-RAY DIFFRACTION	r_angle_refined_deg	1.518	1.633	28965
X-RAY DIFFRACTION	r_angle_other_deg	0.418	1.57	45106
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.131	5	2736
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.35	23.793	986
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.979	15	3422
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.935	15	83
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	2691
X-RAY DIFFRACTION	r_gen_planes_refined	0.054	0.02	24008
X-RAY DIFFRACTION	r_gen_planes_other	0.051	0.02	4065
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	4047
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	18738
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	10404
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.095	0.2	10334
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.191	0.2	1122
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.121	0.2	8
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.395	0.2	132
X-RAY DIFFRACTION	r_nbd_other	0.331	0.2	238
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.444	0.2	46
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.024	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	6.771	6.477	10884
X-RAY DIFFRACTION	r_mcbond_other	6.766	6.476	10883
X-RAY DIFFRACTION	r_mcangle_it	8.937	12.08	13589
X-RAY DIFFRACTION	r_mcangle_other	8.938	12.083	13590
X-RAY DIFFRACTION	r_scbond_it	9.721	7.924	10370
X-RAY DIFFRACTION	r_scbond_other	9.714	7.921	10368
X-RAY DIFFRACTION	r_scangle_it	13.199	14.041	15359
X-RAY DIFFRACTION	r_scangle_other	13.199	14.042	15359
X-RAY DIFFRACTION	r_lrange_it	15.961	43.605	23147
X-RAY DIFFRACTION	r_lrange_other	15.996	43.545	22977
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.053	0.05	6953
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.043	0.05	6974
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.04	0.05	6977
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.055	0.05	6947
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.042	0.05	6988
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.06	0.05	6899
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.043	0.05	5043
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.087	0.05	4900
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.038	0.05	5040
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.038	0.05	5039
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.053	0.05	5001
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.055	0.05	5014
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.046	0.05	6992
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.045	0.05	6974
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.051	0.05	6968
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.047	0.05	6991
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.062	0.05	6933
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.091	0.05	4919
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.046	0.05	5035
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.041	0.05	5059
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.058	0.05	5008
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.049	0.05	5042
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.03	0.05	7019
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.047	0.05	6941
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.033	0.05	7009
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.052	0.05	6934
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.086	0.05	4886
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.086	0.05	4884
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.079	0.05	4899
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.089	0.05	4907
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.04	0.05	6892
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.024	0.05	6951
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.05	0.05	6888
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.03	0.05	5060
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.049	0.05	5019
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.05	0.05	5007
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.05	0.05	6953
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.063	0.05	6889
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.043	0.05	5037
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.041	0.05	5030
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.053	0.05	6917
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.055	0.05	5001

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.154	0.392	32	0.306	3758	X-RAY DIFFRACTION	26.1994
2.154-2.213	0.286	75	0.287	7158	X-RAY DIFFRACTION	51.1745
2.213-2.277	0.294	100	0.268	9264	X-RAY DIFFRACTION	68.1117
2.277-2.347	0.286	82	0.253	10526	X-RAY DIFFRACTION	79.111
2.347-2.424	0.245	130	0.241	11657	X-RAY DIFFRACTION	90.8019
2.424-2.509	0.282	118	0.225	11871	X-RAY DIFFRACTION	95.8736
2.509-2.603	0.229	105	0.211	11895	X-RAY DIFFRACTION	98.8631
2.603-2.709	0.22	144	0.192	11500	X-RAY DIFFRACTION	99.7687
2.709-2.83	0.251	111	0.186	11036	X-RAY DIFFRACTION	99.9283
2.83-2.967	0.226	115	0.192	10582	X-RAY DIFFRACTION	99.9533
2.967-3.127	0.239	94	0.192	10079	X-RAY DIFFRACTION	99.9312
3.127-3.316	0.218	97	0.19	9558	X-RAY DIFFRACTION	99.9482
3.316-3.544	0.19	79	0.189	8999	X-RAY DIFFRACTION	99.835
3.544-3.826	0.209	87	0.176	8329	X-RAY DIFFRACTION	99.7275
3.826-4.189	0.168	78	0.152	7694	X-RAY DIFFRACTION	99.9229
4.189-4.679	0.124	52	0.124	6986	X-RAY DIFFRACTION	99.9006
4.679-5.395	0.17	54	0.132	6179	X-RAY DIFFRACTION	99.8878
5.395-6.589	0.168	39	0.151	5283	X-RAY DIFFRACTION	99.8499
6.589-9.238	0.19	40	0.154	4070	X-RAY DIFFRACTION	99.5157
9.238-49.494	0.198	18	0.174	2341	X-RAY DIFFRACTION	98.1281

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