PDB-9csj: Crystal structure of human glyoxalase domain-containing protein 4...

ID or keywords:

Entry

Database: PDB / ID: 9csj

Title

Crystal structure of human glyoxalase domain-containing protein 4 (GLOD4) at 2.33 A resolution.

Components

Isoform 2 of Glyoxalase domain-containing protein 4

Keywords

METAL BINDING PROTEIN / Glyoxalase domain-containing protein 4 / metallo-b-lactamase synuclein nitrase

Function / homology

Function and homology information

cadherin binding / mitochondrion / extracellular exosome
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.33 Å

Authors

Griswold-Prenner, I. / Dou, Y. / Jennings, A. / Kayser, F.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of apo-Glyoxalase domain-containing protein 4 (apo-GLOD4) at 2.33 A resolution.
Authors: Griswold-Prenner, I. / Kayser, F.

History

Deposition	Jul 24, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 13, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9csj.cif.gz	360.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9csj.ent.gz	295.8 KB	Display	PDB format
PDBx/mmJSON format	9csj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9csj_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	9csj_full_validation.pdf.gz	1.9 MB	Display
Data in XML	9csj_validation.xml.gz	42.3 KB	Display
Data in CIF	9csj_validation.cif.gz	58.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cs/9csj ftp://data.pdbj.org/pub/pdb/validation_reports/cs/9csj	HTTPS FTP

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Related structure data

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: Isoform 2 of Glyoxalase domain-containing protein 4

B: Isoform 2 of Glyoxalase domain-containing protein 4

C: Isoform 2 of Glyoxalase domain-containing protein 4

hetero molecules

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

1

A: Isoform 2 of Glyoxalase domain-containing protein 4

hetero molecules

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

2

B: Isoform 2 of Glyoxalase domain-containing protein 4

hetero molecules

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

3

C: Isoform 2 of Glyoxalase domain-containing protein 4

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.960, 85.960, 135.900
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	2
3	3

/ NCS ensembles :

ID
1
2
3

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Protein , 1 types, 3 molecules ABC

#1: Protein	Isoform 2 of Glyoxalase domain-containing protein 4 Mass: 33362.844 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLOD4, C17orf25, CGI-150, My027 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HC38

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Non-polymers , 6 types, 497 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.51 Å³/Da / Density % sol: 50.96 %
Crystal grow	Temperature: 291 K / Method: evaporation / pH: 7.3 Details: GLOD4 aa2-298 with an N-terminal 8-His tag was expressed in E. coli, purified by IMAC and SEC, and stored in 50 mM HEPES (pH 7.5), 500 mM NaCl, and 5% glycerol at -80 C. His-GLOD4 (18 mg/ml) ...Details: GLOD4 aa2-298 with an N-terminal 8-His tag was expressed in E. coli, purified by IMAC and SEC, and stored in 50 mM HEPES (pH 7.5), 500 mM NaCl, and 5% glycerol at -80 C. His-GLOD4 (18 mg/ml) was crystallized after Hist-tag removal in 34% PEG 3350, 200 mM MgCl2, and 50 mM HEPES, pH 7.3.

Crystal

Density Matthews: 2.51 Å³/Da / Density % sol: 50.96 %

Crystal grow

Temperature: 291 K / Method: evaporation / pH: 7.3
Details: GLOD4 aa2-298 with an N-terminal 8-His tag was expressed in E. coli, purified by IMAC and SEC, and stored in 50 mM HEPES (pH 7.5), 500 mM NaCl, and 5% glycerol at -80 C. His-GLOD4 (18 mg/ml) ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 6, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.33→45.34 Å / Num. obs: 42055 / % possible obs: 99.9 % / Redundancy: 14.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.163 / R_pim(I) all: 0.045 / R_rim(I) all: 0.169 / Χ²: 1.02 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.33→2.41 Å / Redundancy: 13.3 % / R_merge(I) obs: 1.253 / Num. unique obs: 4088 / CC_1/2: 0.842 / R_pim(I) all: 0.354 / Χ²: 0.96

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.33→45.34 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.899 / SU B: 16.068 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26902	2091	5 %	RANDOM
R_work	0.22013	-	-	-
obs	0.22267	39964	99.93 %	-

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: 48.588 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.45 Å²	-0 Å²	-0 Å²
2-	-	1.45 Å²	-0 Å²
3-	-	-	-2.91 Å²

Refinement step

Cycle: 1 / Resolution: 2.33→45.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6832	0	64	473	7369

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	7093
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6675
X-RAY DIFFRACTION	r_angle_refined_deg	1.502	1.644	9570
X-RAY DIFFRACTION	r_angle_other_deg	1.238	1.588	15437
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.161	5	875
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.441	23.351	376
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.357	15	1236
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.02	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	851
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8055
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1609
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	2.273	4.014	3497
X-RAY DIFFRACTION	r_mcbond_other	2.273	4.013	3496
X-RAY DIFFRACTION	r_mcangle_it	3.613	6.006	4373
X-RAY DIFFRACTION	r_mcangle_other	3.612	6.007	4374
X-RAY DIFFRACTION	r_scbond_it	2.192	4.269	3596
X-RAY DIFFRACTION	r_scbond_other	2.191	4.27	3597
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.538	6.309	5198
X-RAY DIFFRACTION	r_long_range_B_refined	6.2	45.666	7571
X-RAY DIFFRACTION	r_long_range_B_other	6.151	45.502	7499
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	9366	0.07
1	2	B	9366	0.07
2	1	A	8289	0.12
2	2	C	8289	0.12
3	1	B	8301	0.11
3	2	C	8301	0.11

LS refinement shell

Resolution: 2.33→2.391 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.286	157	-
R_work	0.268	2920	-
obs	-	-	99.77 %

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	0.2649	-0.1339	-0.14	1.0173	-0.4132	0.4478	0.0314	-0.0024	0.0407	-0.0529	0.0033	0.0461	0.0686	-0.0311	-0.0346	0.1224	-0.0107	-0.005	0.0784	0.0028	0.0335	27.4789	24.9828	-51.2925
2	1.2705	-2.0628	0.5561	3.5499	-1.3787	1.3852	-0.1019	-0.0159	0.2871	0.2292	0.0498	-0.4453	-0.2319	-0.0652	0.0521	0.1808	0.0214	-0.0006	0.0609	-0.0057	0.1159	26.413	40.9331	-45.9823
3	0.7614	-0.3518	0.2924	0.5623	0.4026	0.9225	0.0134	0.0193	0.0388	-0.1015	0.0441	-0.0352	-0.0259	0.0612	-0.0576	0.1609	-0.0386	-0.0181	0.07	0.0144	0.0485	29.5826	23.3421	-57.636
4	0.137	0.035	0.0324	0.1704	-0.01	0.5659	-0.017	-0.0217	0.0221	-0.1026	0.0407	0.0102	0.153	0.1057	-0.0237	0.176	0.022	0.0124	0.081	-0.0111	0.0158	41.8554	16.637	-58.3287
5	0.8393	0.3086	-0.2232	0.2107	-0.2815	0.5223	0.0375	-0.0582	0.0597	0.0001	-0.0416	0.0298	0.0026	0.1009	0.0041	0.1241	-0.0002	-0.0053	0.0967	-0.0078	0.0408	42.9099	28.0294	-42.3804
6	0.1444	-0.3979	0.0784	1.1041	-0.2081	0.0932	0.0057	0.0107	-0.0141	-0.0058	-0.0374	0.0465	-0.0177	0.0464	0.0318	0.1519	-0.0124	-0.0032	0.0768	0.0235	0.0504	18.9737	37.0956	-51.8498
7	0.7688	-0.037	-0.3566	0.0231	-0.0635	0.4835	0.0158	0.0046	0.0419	0.0048	-0.0047	-0.0055	0.0031	0.0233	-0.0111	0.0893	-0.0049	0.0051	0.1361	-0.0042	0.0397	17.4847	15.8181	-16.8901
8	2.6985	-0.709	-1.2145	0.3087	0.0918	1.0282	0.0483	0.2841	-0.2077	-0.0251	-0.0299	0.0879	-0.0463	-0.1826	-0.0183	0.0719	0.0183	0.0228	0.1761	-0.0185	0.0761	2.1486	16.4181	-22.4937
9	0.1633	0.0259	0.099	0.4575	0.0823	0.5393	0.0511	-0.0784	0.0242	0.0028	-0.0254	0.046	0.0803	0.0963	-0.0257	0.0754	0.0002	0.0027	0.161	0.003	0.024	24.1568	5.101	-10.4515
10	0.4487	0.1209	-0.3549	0.8815	-0.2528	0.3174	-0.0366	-0.0256	0.0041	-0.0438	0.0302	0.0274	0.0509	0.0165	0.0065	0.1053	-0.0047	-0.0078	0.1331	-0.0068	0.0319	14.9487	0.0104	-26.2046
11	1.8538	-0.3024	-0.5375	0.072	0.1079	0.3906	0.0495	-0.0416	0.1637	-0.0254	-0.0122	-0.0056	-0.0402	0.0177	-0.0372	0.0712	-0.0069	0.0077	0.1232	0.0027	0.0507	5.9491	23.9916	-16.6226
12	0.5531	-0.7908	-0.6361	1.1868	0.932	0.7418	0.1897	0.1322	-0.1075	-0.3139	-0.2786	0.121	-0.2619	-0.1782	0.0889	0.2419	0.0516	-0.0399	0.1487	-0.0002	0.0457	52.4393	-13.8145	-43.7963
13	0.0176	-0.1495	0.0954	1.3115	-0.9721	1.2903	0.0258	0.0021	-0.0162	-0.218	-0.0073	0.1404	0.056	-0.0027	-0.0186	0.0757	-0.0198	-0.0103	0.0761	-0.0042	0.0969	53.5899	-12.8161	-44.2074
14	0.3902	0.5379	-0.3576	0.7851	-0.086	5.9829	-0.091	-0.041	-0.0955	-0.1043	-0.0206	-0.1325	-0.012	0.1337	0.1116	0.0839	0.0639	0.0327	0.0676	0.0052	0.0478	54.4048	-0.1339	-39.793
15	2.8329	0.9212	0.4055	5.7717	-3.7254	2.7824	0.0544	0.6077	-0.1737	0.7272	0.0442	0.0922	-0.4689	0.2015	-0.0987	0.2189	-0.0014	0.1324	0.1365	-0.0344	0.1236	56.1764	3.8137	-25.569
16	1.5432	-0.441	-0.9796	1.7756	-0.4102	0.9355	0.1659	0.0658	0.0188	0.041	-0.0344	0.2566	-0.0826	0.0098	-0.1315	0.1943	0.1092	-0.001	0.0872	-0.0196	0.0462	52.2313	-9.1849	-25.5868
17	1.0605	-1.4542	-2.6952	2.1706	4.0729	7.7524	0.3256	0.2934	0.0647	-0.2387	-0.3683	-0.0543	-0.3593	-0.7398	0.0427	0.3148	0.0889	0.0892	0.1345	-0.0202	0.1695	49.1675	-21.4348	-25.2623
18	1.4874	-1.186	-2.0702	4.4791	1.1665	2.9557	-0.1648	0.0141	-0.1451	0.0578	-0.0054	0.2156	0.2487	-0.0273	0.1702	0.1488	0.0442	0.0032	0.0306	0.019	0.0594	53.7756	-17.0611	-27.0204
19	5.5724	2.0826	1.2686	1.088	0.6393	1.2011	-0.2384	-0.1216	-1.1884	-0.3284	0.2676	-0.405	-0.764	-0.1034	-0.0292	0.5906	-0.0425	-0.1056	0.3231	0.0094	0.3022	48.4645	-26.4152	-51.0551

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 38
2	X-RAY DIFFRACTION	2	A	39 - 59
3	X-RAY DIFFRACTION	3	A	60 - 103
4	X-RAY DIFFRACTION	4	A	104 - 188
5	X-RAY DIFFRACTION	5	A	189 - 264
6	X-RAY DIFFRACTION	6	A	265 - 298
7	X-RAY DIFFRACTION	7	B	2 - 38
8	X-RAY DIFFRACTION	8	B	39 - 59
9	X-RAY DIFFRACTION	9	B	60 - 188
10	X-RAY DIFFRACTION	10	B	189 - 264
11	X-RAY DIFFRACTION	11	B	265 - 298
12	X-RAY DIFFRACTION	12	C	4 - 25
13	X-RAY DIFFRACTION	13	C	26 - 102
14	X-RAY DIFFRACTION	14	C	103 - 157
15	X-RAY DIFFRACTION	15	C	158 - 176
16	X-RAY DIFFRACTION	16	C	177 - 220
17	X-RAY DIFFRACTION	17	C	221 - 239
18	X-RAY DIFFRACTION	18	C	240 - 264
19	X-RAY DIFFRACTION	19	C	265 - 293

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