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

Basic information

• 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:

amelogenesis / endopeptidase inhibitor activity / extracellular matrix disassembly / protein catabolic process / serine-type endopeptidase activity / proteolysis / extracellular space

Domain/homology:

Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan

Component:

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

• 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.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

Assembly

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

Summary:

• 294 kDa, 14 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	294,466	14
Polymers	294,466	14
Non-polymers	0	0
Water	24,122	1339

1

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

B: Kunitz-type inihibitor

Summary:

• defined by author&software
• Evidence: gel filtration
• 42.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	42,067	2
Polymers	42,067	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1910 Å2
ΔGint	-12 kcal/mol
Surface area	16290 Å2
Method	PISA

2

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

D: Kunitz-type inihibitor

Summary:

• defined by author&software
• 42.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	42,067	2
Polymers	42,067	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1910 Å2
ΔGint	-12 kcal/mol
Surface area	16400 Å2
Method	PISA

3

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

F: Kunitz-type inihibitor

Summary:

• defined by author&software
• 42.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	42,067	2
Polymers	42,067	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1980 Å2
ΔGint	-12 kcal/mol
Surface area	16260 Å2
Method	PISA

4

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

H: Kunitz-type inihibitor

Summary:

• defined by author&software
• 42.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	42,067	2
Polymers	42,067	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1940 Å2
ΔGint	-12 kcal/mol
Surface area	16230 Å2
Method	PISA

5

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

J: Kunitz-type inihibitor

Summary:

• defined by author&software
• 42.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	42,067	2
Polymers	42,067	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1900 Å2
ΔGint	-12 kcal/mol
Surface area	16340 Å2
Method	PISA

6

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

L: Kunitz-type inihibitor

Summary:

• defined by author&software
• 42.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	42,067	2
Polymers	42,067	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1910 Å2
ΔGint	-12 kcal/mol
Surface area	16350 Å2
Method	PISA

7

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

N: Kunitz-type inihibitor

Summary:

• defined by author&software
• 42.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	42,067	2
Polymers	42,067	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1930 Å2
ΔGint	-13 kcal/mol
Surface area	16240 Å2
Method	PISA

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:

ID	Ens-ID	Details
1	1	Chains A C
2	1	Chains A E
3	1	Chains A G
4	1	Chains A I
5	1	Chains A K
6	1	Chains A M
7	1	Chains B D
8	1	Chains B F
9	1	Chains B H
10	1	Chains B J
11	1	Chains B L
12	1	Chains B N
13	1	Chains C E
14	1	Chains C G
15	1	Chains C I
16	1	Chains C K
17	1	Chains C M
18	1	Chains D F
19	1	Chains D H
20	1	Chains D J
21	1	Chains D L
22	1	Chains D N
23	1	Chains E G
24	1	Chains E I
25	1	Chains E K
26	1	Chains E M
27	1	Chains F H
28	1	Chains F J
29	1	Chains F L
30	1	Chains F N
31	1	Chains G I
32	1	Chains G K
33	1	Chains G M
34	1	Chains H J
35	1	Chains H L
36	1	Chains H N
37	1	Chains I K
38	1	Chains I M
39	1	Chains J L
40	1	Chains J N
41	1	Chains K M
42	1	Chains L N

Components

#1: Protein

A C E G I K M
Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a / Kallikrein B1 / Kallikrein-4

Details:

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

B D F H J L N
Kunitz-type inihibitor

Details:

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 / Water

Details:

Mass: 18.015 Da / Num. of mol.: 1339 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.92 ų/Da / Density % sol: 57.92 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 0.2M NaCl

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

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

	Rfactor	Num. reflection	% reflection
Rfree	0.2122	1650	0.968 %
Rwork	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 Ų

	Baniso -1	Baniso -2	Baniso -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)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	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