PDB-7f88: Crystal structure of GH19 chitinase lacking the third loop structure

ID or keywords:

Entry

Database: PDB / ID: 7f88

Title

Crystal structure of GH19 chitinase lacking the third loop structure

Components

Chitinase A

Keywords

HYDROLASE / chitinase

Function / homology

Function and homology information

chitinase activity / chitin catabolic process / defense response to fungus / cell wall macromolecule catabolic process / carbohydrate metabolic process
Similarity search - Function

Biological species

Gemmabryum coronatum (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Ohnuma, T. / Numata, T.

Citation

Journal: Glycobiology / Year: 2022
Title: A conserved loop structure of GH19 chitinases assists the enzyme function from behind the core-functional region.
Authors: Kawamoto, D. / Takashima, T. / Fukamizo, T. / Numata, T. / Ohnuma, T.

History

Deposition	Jul 1, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 13, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7f88.cif.gz	284.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7f88.ent.gz	189 KB	Display	PDB format
PDBx/mmJSON format	7f88.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7f88_validation.pdf.gz	446.9 KB	Display	wwPDB validaton report
Full document	7f88_full_validation.pdf.gz	447.7 KB	Display
Data in XML	7f88_validation.xml.gz	25.7 KB	Display
Data in CIF	7f88_validation.cif.gz	38.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f8/7f88 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/7f88	HTTPS FTP

-
Related structure data

Related structure data	3wh1S S: Starting model for refinement
Similar structure data	2anq-d 5zj5-2 4x5f-1 3mer-1 5fjq-1 5uiz-2 3q6z-d 2inq-2 3qyo-d 5fjq-3 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

3wh1S

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Chitinase A

B: Chitinase A

C: Chitinase A

66 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chitinase A

defined by author
Evidence: gel filtration
22 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Chitinase A

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

3

C: Chitinase A

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

Unit cell

Length a, b, c (Å)	116.260, 103.647, 45.418
Angle α, β, γ (deg.)	90.000, 95.069, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	C-364- HOH
2	1	C-404- HOH

#1: Protein	Chitinase A Mass: 21990.152 Da / Num. of mol.: 3 / Mutation: Deletion of loop III, E84A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gemmabryum coronatum (plant) / Gene: bcchiA / Production host: Escherichia coli (E. coli) / References: UniProt: A9ZSX9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium citrate dibasic, 20 % w/v polyethylene glycol 3350, pH 5.1

-
Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 70086 / % possible obs: 99.4 % / Redundancy: 6.5 % / B_iso Wilson estimate: 14.32 Å² / R_merge(I) obs: 0.068 / R_pim(I) all: 0.029 / Net I/σ(I): 20.7
Reflection shell	Resolution: 1.6→1.63 Å / R_merge(I) obs: 0.427 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3458 / R_pim(I) all: 0.191

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3WH1

3wh1

Resolution: 1.6→45.24 Å / SU ML: 0.1277 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.2214
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1751	3436	4.91 %
R_work	0.1459	66607	-
obs	0.1474	70043	99.35 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 18.46 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→45.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4360	0	0	489	4849

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0124	4546
X-RAY DIFFRACTION	f_angle_d	1.1527	6218
X-RAY DIFFRACTION	f_chiral_restr	0.0698	642
X-RAY DIFFRACTION	f_plane_restr	0.0085	835
X-RAY DIFFRACTION	f_dihedral_angle_d	5.3438	633

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 (%)
1.6-1.62	0.2246	147	0.1798	2635	X-RAY DIFFRACTION	96.43
1.62-1.65	0.1985	128	0.1773	2573	X-RAY DIFFRACTION	99.08
1.65-1.67	0.252	138	0.1679	2650	X-RAY DIFFRACTION	99.11
1.67-1.7	0.2219	145	0.1621	2646	X-RAY DIFFRACTION	98.62
1.7-1.72	0.1882	145	0.1583	2635	X-RAY DIFFRACTION	99.46
1.72-1.75	0.2063	116	0.1515	2696	X-RAY DIFFRACTION	98.77
1.75-1.79	0.196	137	0.1558	2646	X-RAY DIFFRACTION	99.64
1.79-1.82	0.1957	139	0.1492	2677	X-RAY DIFFRACTION	99.02
1.82-1.86	0.1756	138	0.1535	2653	X-RAY DIFFRACTION	99.79
1.86-1.9	0.1897	125	0.1526	2664	X-RAY DIFFRACTION	99.25
1.9-1.94	0.188	141	0.1441	2639	X-RAY DIFFRACTION	99.71
1.94-1.99	0.1722	148	0.1405	2675	X-RAY DIFFRACTION	99.26
1.99-2.04	0.181	130	0.1407	2635	X-RAY DIFFRACTION	99.5
2.04-2.1	0.1779	151	0.1394	2653	X-RAY DIFFRACTION	99.4
2.1-2.17	0.1588	139	0.1339	2646	X-RAY DIFFRACTION	98.76
2.17-2.25	0.192	128	0.1365	2684	X-RAY DIFFRACTION	99.54
2.25-2.34	0.1642	146	0.1342	2636	X-RAY DIFFRACTION	99.93
2.34-2.45	0.1846	132	0.1384	2704	X-RAY DIFFRACTION	99.96
2.45-2.57	0.1693	145	0.1425	2685	X-RAY DIFFRACTION	99.96
2.57-2.74	0.1673	119	0.1458	2689	X-RAY DIFFRACTION	100
2.74-2.95	0.1658	155	0.1522	2663	X-RAY DIFFRACTION	100
2.95-3.24	0.1972	151	0.1461	2716	X-RAY DIFFRACTION	100
3.24-3.71	0.1557	127	0.1396	2683	X-RAY DIFFRACTION	99.93
3.71-4.68	0.1332	118	0.1302	2709	X-RAY DIFFRACTION	99.93
4.68-45.24	0.1739	148	0.1681	2715	X-RAY DIFFRACTION	98.93

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.20624652057	0.428316984028	0.477227207715	1.42958618584	0.808128395031	2.49543786876	0.0252864530341	0.0188294471337	-0.129474149692	0.168318882906	-0.0340956167428	-0.00455368306574	0.413825081434	-0.0716673344655	0.00964480469163	0.16829217479	0.0101276403141	0.0224687270499	0.107065381018	0.0132876032671	0.103258008421	17.4131921501	-11.5911760012	17.2288580874
2	3.04340003684	-0.147125705125	-0.647082853665	6.80396111519	-0.403419768017	2.71144581499	0.173903716748	0.603287199011	0.0906179138039	-0.23961478467	-0.000764307786738	0.300753627315	0.285764352675	-1.17742120001	-0.229839734911	0.144254743189	-0.0483356641478	0.0298731077977	0.427624169527	-0.00999562334131	0.205569334705	5.13612023496	-12.2861372907	2.85203426679
3	1.61559415232	0.87505513019	-0.174455810522	2.37657896234	0.0381351071749	3.408131037	-0.0130291518244	0.0285004153812	-0.0336271589082	-0.00722983690449	-0.00451306268714	0.0686911862541	0.109178246988	-0.205936353843	0.00162272132525	0.111127470494	0.0105467065582	0.0165500469182	0.119108858616	-0.00643343509563	0.101333817693	16.9617877072	-9.54667911142	-2.08437214081
4	1.91929826028	-0.235335248331	-1.54053568348	2.85053010004	0.723310666362	2.23860792218	0.00771239588354	0.128156692236	0.106819922462	0.0769129875152	0.0161629938139	0.119803065555	-0.121195284455	-0.216924389572	0.00406813999032	0.1241360748	0.0206699934158	0.0146682267584	0.100931751208	0.0174282495834	0.0860678461315	18.1726837393	3.02996067753	12.2314018222
5	2.20965730905	-0.391014570363	0.304869808881	2.89256392835	-1.16482149374	2.76648466942	-0.00166080018106	0.130642958277	0.114456254878	0.0267082420373	0.0962402065541	0.252194171387	-0.0579259031662	-0.318780849829	-0.0880501298501	0.109856234372	0.0216483477814	0.0273892065138	0.162817013204	0.000256767380754	0.109372210457	7.71387478888	2.51532184053	18.4111345755
6	9.13205834611	-2.49342865106	-0.336575182143	4.91418291452	0.139267550897	8.82268602958	0.0209959244948	0.0691007845047	0.0571456521305	-0.17820245389	-0.0665869501896	-0.485780143669	-0.0458935064332	0.356206347481	0.0537241450982	0.128229717123	-0.0209166381577	0.026138073515	0.140369686079	-0.00121413582552	0.140619237133	36.6167565087	18.6401194442	-9.38138252103
7	1.31813790808	-0.179195540777	0.0905530653833	1.2914985269	0.56241503294	1.52240910907	0.0303585145433	-0.045239170645	0.0347264197014	-0.0966362338439	-0.00375550979589	-0.109333638468	-0.016771451171	0.109852784849	-0.0315279598038	0.149794599049	0.00250523532181	0.0174870878072	0.111016569386	0.0242910842541	0.128201100598	32.6752026323	16.0143551407	-3.38174677724
8	0.279364992344	-0.303628460907	0.377202849164	4.46828580545	-3.85699966772	3.3807815156	-0.00763326648686	-0.13508923628	0.00785375855302	0.253605230444	0.108754372253	0.104123261981	-0.450795809472	-0.475998575218	-0.0867175105399	0.175291271771	0.0102564101456	0.0151737529157	0.156100067046	0.00231271860593	0.1832553393	24.8890896182	26.3962634486	6.72198232986
9	2.00326243882	1.34881245617	-1.2334974863	2.91772710581	-0.418623333249	2.10597196115	0.0797218520255	0.0142836799638	0.133678338998	0.261610831105	0.00984415577163	0.0610297569194	-0.205674156725	0.0638794817428	-0.088773121684	0.193031131804	0.012076604225	-0.00480776275685	0.123600933368	0.014722442663	0.117646367931	28.4531542568	16.804349985	15.4566860869
10	1.16894545117	0.630210934391	0.321908832563	1.05493257524	0.187350232959	1.07286920591	-0.0474212347652	0.00167017963941	0.0107525375132	-0.0511210064955	0.0192938854603	0.0312030723745	-0.0213473479558	-0.00168393142024	0.0209364715457	0.1701092806	0.015654311287	0.0165886913248	0.107369618024	0.0117095416619	0.118221576946	24.7697573831	9.62568876601	1.24356942452
11	5.74399852534	-0.861569875289	-2.56547819327	1.2205185173	1.20336631036	1.88566713285	-0.00185888551932	0.0290719494946	0.153731703711	-0.0749679836432	-0.00430851537584	0.12802570434	-0.0530333185749	-0.0706306640126	-0.00839214566648	0.191012428087	0.0201474904367	-0.0158616952924	0.0988043186686	0.0195903794957	0.105763895064	16.6722025211	15.4864073184	-8.5890768647
12	2.91619832693	0.111126142868	-1.00712256442	1.28614107242	-0.488206347595	3.55217921543	-0.0347123626445	0.0972531270211	0.0555021618956	-0.0764217580047	-0.0143865809785	0.0297208523165	-0.073755407848	0.00357528496081	0.0307368127587	0.104547189175	0.0284751946537	-0.0178722481975	0.0812772426101	0.00917673297991	0.0910164835224	38.5846670069	-8.23198500676	-14.8364735528
13	2.33250109353	0.506018456567	-0.696466841728	0.849296825068	0.356572116524	1.72292815383	-0.0231762066739	0.0326635970064	-0.000410594384099	0.0910879313062	-0.0168610998304	-0.0260000859865	-0.1032148842	-0.0280850093505	0.0310656882666	0.140354250846	0.0133004352082	-0.0383718294018	0.0820079167504	0.00986506799255	0.0843956857396	45.0542961161	-8.93914377092	-9.36993750015
14	5.34411415028	-2.37279046275	0.938364637631	2.42502186951	2.36523213269	5.81138629338	0.0574692023792	-0.026030292315	-0.316051315408	0.0451273659022	0.0138948923707	0.0160333693266	0.471378626563	0.067687868574	-0.0399542628738	0.155400348065	-0.012636735893	-0.0179958265147	0.0660427716485	-0.015720837244	0.156468947549	42.4357718028	-15.8189990372	7.03347687499
15	1.32399305031	0.0968381415309	-0.765889474173	0.373051733765	-0.0657227987866	1.6269427372	0.0297546394437	-0.0083345258229	0.0398159786615	0.0217770908167	-0.0123712156217	0.00306387521075	-0.161875168516	0.00497735676418	-0.0269650170298	0.134026485413	0.00602307078132	-0.0198913047782	0.09245476985	0.00184568174407	0.0946734750402	48.6121278693	-8.52863408999	0.141503550892
16	1.59875480486	-0.579555501095	0.317457713214	3.45475136668	-1.28519575562	0.63662778619	0.018271757199	0.00869194781128	-0.161483407985	0.104068721167	-0.0107277301479	0.0417638666867	0.0409358818964	0.00630500924851	-0.00736665064293	0.14070513028	-0.00554728837517	0.007490965394	0.139114067048	-0.0141263949021	0.118137860075	52.1127995194	-21.8482026507	-14.0127742541

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 2 through 62 )	A	A	2 - 62	1 - 61
2	2	chain 'A' and (resid 63 through 72 )	A	A	63 - 72	62 - 72
3	3	chain 'A' and (resid 73 through 139 )	A	A	73 - 139	73 - 130
4	4	chain 'A' and (resid 140 through 168 )	A	A	140 - 168	131 - 159
5	5	chain 'A' and (resid 169 through 205 )	A	A	169 - 205	160 - 196
6	6	chain 'B' and (resid 1 through 15 )	B	B	1 - 15	1 - 17
7	7	chain 'B' and (resid 16 through 61 )	B	B	16 - 61	18 - 67
8	8	chain 'B' and (resid 62 through 76 )	B	B	62 - 76	68 - 77
9	9	chain 'B' and (resid 92 through 128 )	B	B	92 - 128	78 - 116
10	10	chain 'B' and (resid 129 through 168 )	B	B	129 - 168	117 - 156
11	11	chain 'B' and (resid 169 through 205 )	B	B	169 - 205	157 - 193
12	12	chain 'C' and (resid -1 through 24 )	C	C	-1 - 24	1 - 26
13	13	chain 'C' and (resid 25 through 74 )	C	C	25 - 74	27 - 74
14	14	chain 'C' and (resid 75 through 103 )	C	C	75 - 103	75 - 88
15	15	chain 'C' and (resid 104 through 163 )	C	C	104 - 163	89 - 150
16	16	chain 'C' and (resid 164 through 205 )	C	C	164 - 205	151 - 194

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi