SAXSdb — 1d3a

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1. Protein Identity and Related Structures Protein Identity & Related Structures

HALOPHILIC MALATE DEHYDROGENASE

Haloarcula marismortui

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–304 Chain B； UniProt 2–304	Not recorded	CL CHLORIDE ION × 4 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；298 K；MPD-NaCl-H2O system, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.94 Å R-free 0.244

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1D3A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HLP STRUCTURAL FEATURES STABILIZING HALOPHILIC MALATE DEHYDROGENASE FROM AN ARCHAEBACTERIUM Deposited 1994-10-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–304（303 aa） Chain B 2–304（303 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.280
1O6Z 1.95 A resolution structure of (R207S,R292S) mutant of malate dehydrogenase from the halophilic archaeon Haloarcula marismortui (holo form) Deposited 2002-10-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–64（63 aa） Chain A 65–84（20 aa） Chain A 85–194（110 aa） Chain A 195–256（62 aa） Chain A 257–274（18 aa） Chain A 275–304（30 aa） Chain B 2–64（63 aa） Chain B 65–84（20 aa） Chain B 85–194（110 aa） Chain B 195–256（62 aa） Chain B 257–274（18 aa） Chain B 275–304（30 aa） Chain C 2–64（63 aa） Chain C 65–84（20 aa） Chain C 85–194（110 aa） Chain C 195–256（62 aa） Chain C 257–274（18 aa） Chain C 275–304（30 aa） Chain D 2–64（63 aa） Chain D 65–84（20 aa） Chain D 85–194（110 aa） Chain D 195–256（62 aa） Chain D 257–274（18 aa） Chain D 275–304（30 aa）	Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES	CL CHLORIDE ION × 8 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；2 M NACL, 25 MM TRIS PH 7.6, 2.5 MM NADH, 50% MPD	Resolution 1.95 Å R-free 0.263
2HLP CRYSTAL STRUCTURE OF THE E267R MUTANT OF A HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM Deposited 1999-04-23	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–304（303 aa） Chain B 2–304（303 aa）	Mutation：E267R Mutation：E267R	CL CHLORIDE ION × 4 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；1.7M NACL, 20MM TRIS, PH 7.6, 57% MPD	Resolution 2.59 Å R-free 0.236
2J5K 2.0 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui (radiation damage series) Deposited 2006-09-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–304（304 aa） Chain B 1–304（304 aa） Chain C 1–304（304 aa） Chain D 1–304（304 aa）	Not recorded	CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；3UL OF PROTEIN PLUS 4UL OF MPD WERE EQUILIBRATED AGAINST 58% MPD VIA THE SITTING DROP REVERSE VAPOUR DIFFUSION TECHNIQUE, pH 7.00	Resolution 2.00 Å R-free 0.270
2J5Q 2.15 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui after first radiation burn (radiation damage series) Deposited 2006-09-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–304（304 aa） Chain B 1–304（304 aa） Chain C 1–304（304 aa） Chain D 1–304（304 aa）	Not recorded	CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；3UL OF PROTEIN PLUS 4UL OF MPD WERE EQUILIBRATED AGAINST 58% MPD VIA THE SITTING DROP REVERSE VAPOUR DIFFUSION TECHNIQUE, pH 7.00	Resolution 2.15 Å R-free 0.267
2J5R 2.25 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui after second radiation burn (radiation damage series) Deposited 2006-09-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–304（304 aa） Chain B 1–304（304 aa） Chain C 1–304（304 aa） Chain D 1–304（304 aa）	Not recorded	CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；3UL OF PROTEIN PLUS 4UL OF MPD WERE EQUILIBRATED AGAINST 58% MPD VIA THE SITTING DROP REVERSE VAPOUR DIFFUSION TECHNIQUE, pH 7.00	Resolution 2.25 Å R-free 0.271
2X0R R207S, R292S Mutant of Malate Dehydrogenase from the Halophilic Archeon Haloarcula marismortui (HoloForm) Deposited 2009-12-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–304（304 aa） Chain B 1–304（304 aa）	Mutation：YES Mutation：YES	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 CL CHLORIDE ION × 8 NA SODIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；2 M NACL, 25 MM TRIS PH 7.6, 2.5 MM NADH, 50% MPD	Resolution 2.92 Å R-free 0.286
4JCO 1.7 A resolution structure of wild type malate dehydrogenase from haloarcula marismortui Deposited 2013-02-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–304（304 aa） Chain B 1–304（304 aa） Chain C 1–304（304 aa） Chain D 1–304（304 aa）	Not recorded	CL CHLORIDE ION × 13 NA SODIUM ION × 26	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；58% MPD, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.257
7Q3X Crystal structure of Malate dehydrogenase from Haloarcula marismortui with Potassium and Chloride ions Deposited 2021-10-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–304（303 aa） Chain B 2–304（303 aa） Chain C 2–304（303 aa） Chain D 2–304（303 aa）	Not recorded	CL CHLORIDE ION × 28 K POTASSIUM ION × 21	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；Protein: 10mg/ml, 50mM Tris pH 7, 2M KCl Cristal Growth: 100mM Tris pH 7.5-7.6 + 60-66% MPD	Resolution 1.95 Å R-free 0.246

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MDH_HALMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–303； UniProt 2–304 Author chain B； PDBConstruct 1–303； UniProt 2–304

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d3a
Deposition date deposition_date	1999-09-28
Structure title title	CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM
Keywords keywords	ROSSMANN FOLD AND 3 SORTS OF COMPLEX SALT BRIDGES, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.80 Å
Radius of gyration Rg (electron density) rg_electron	25.70 Å
Forward intensity I(0) i0	78314000.00
Molecular weight molecular_weight	65369.0 kDa
Excluded volume excluded_volume	80079 Å³
Envelope volume envelope_volume	97792 Å³
Hydration-shell volume shell_volume	31492 Å³
Envelope diameter envelope_diameter	87.0 Å
Shell Rg shell_rg	33.26 Å
Envelope Rg envelope_rg	25.73 Å
Shape Rg shape_rg	25.72 Å
Total Rg total_rg	26.41 Å
Total atoms total_atoms	4605
Residues n_residues	606
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	83.6 Å
Rg (real space) rg_real	26.77 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	7.8310e+07
I(0) uncertainty (real space) i0_real_error	1.0670e+06
Rg (reciprocal space) rg_reciprocal	26.78 Å
I(0) (reciprocal space) i0_reciprocal	78310000.0000
Solution quality estimate total_estimate	0.8961
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.2 Å
Skewness Skewness skewness	0.334
Kurtosis Kurtosis kurtosis	-0.392
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18280000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.875

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	HALOPHILIC MALATE DEHYDROGENASE
Molecular weight formula_weight	32706.5 kDa
EC 编号 ec_number	1.1.1.37
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4637

TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS

来源 Source

来源生物 organism	Haloarcula marismortui
NCBI Class编号 ncbi_taxonomy_id	2238
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1d3aa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.5 — LDH N-terminal domain-like

Domain ID domain_id	d1d3aa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

Domain ID domain_id	d1d3ab1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.5 — LDH N-terminal domain-like

Domain ID domain_id	d1d3ab2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1d3aA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

Domain ID domain_id	1d3aA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1d3aB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

Domain ID domain_id	1d3aB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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8. Citations (5)

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Unit-cell length a length_a	115.780 Å
Unit-cell length b length_b	131.330 Å
Unit-cell length c length_c	125.450 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.940 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2020
R_free r_free	0.2440

fit	/app/data/saxs_computation/d3/1d3a/1d3a.fit
pddf	/app/data/pr_computation/d3/1d3a/1d3a.pr.out
profile	/app/data/saxs_computation/d3/1d3a/1d3a.dat

CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM

1. Protein Identity and Related Structures Protein Identity & Related Structures

HALOPHILIC MALATE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction