SAXSdb — 1civ

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

NADP-MALATE DEHYDROGENASE

OrganismNot specified

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 69–453	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；SEE MACPHERSON ET AL. (1998) ACTA CRYST, D54, 654 - 656, pH 7.50	Resolution 2.80 Å R-free 0.284

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	MDHP_FLABI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–385； UniProt 69–453

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	1civ
Deposition date deposition_date	1999-04-01
Structure title title	CHLOROPLAST NADP-DEPENDENT MALATE DEHYDROGENASE FROM FLAVERIA BIDENTIS
Keywords keywords	CHLOROPLAST, LIGHT ACTIVATED, NADP-DEPENDENT, DEHYDROGENASE, 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	21.20 Å
Radius of gyration Rg (electron density) rg_electron	20.33 Å
Forward intensity I(0) i0	28200700.00
Molecular weight molecular_weight	40626.0 kDa
Excluded volume excluded_volume	50770 Å³
Envelope volume envelope_volume	58150 Å³
Hydration-shell volume shell_volume	23490 Å³
Envelope diameter envelope_diameter	70.8 Å
Shell Rg shell_rg	27.35 Å
Envelope Rg envelope_rg	20.70 Å
Shape Rg shape_rg	20.34 Å
Total Rg total_rg	21.18 Å
Total atoms total_atoms	2853
Residues n_residues	374
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	70.0 Å
Rg (real space) rg_real	21.11 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	2.8200e+07
I(0) uncertainty (real space) i0_real_error	3.9350e+05
Rg (reciprocal space) rg_reciprocal	21.13 Å
I(0) (reciprocal space) i0_reciprocal	28200000.0000
Solution quality estimate total_estimate	0.8790
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.256
Kurtosis Kurtosis kurtosis	-0.324
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8375000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.971

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	NADP-MALATE DEHYDROGENASE
Molecular weight formula_weight	42097.0 kDa
EC 编号 ec_number	1.1.1.82
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2959

SVTSSDQIQAPLPAKQKPECFGVFCLTYDLKAEEETKSWKKIINVAVSGAAGMISNHLLFKLASGEVFGPDQPISLKLLGSERSFAALEGVAMELEDSLYPLLRQVSIGIDPYEIFQDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNAVASPNVKVMVVGNPCNTNALICLKNAPNIPPKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFLNAKIHGIPVTEVIRDRKWLEDEFTNMVQTRGGVLIKKWGRSSAASTAVSIVDAIRSLVTPTPEGDWFSTGVYTNGNPYGIAEDIVFSMPCRSKGDGDYEFVKDVIFDDYLSKKIKKSEDELLAEKKCVAHLTGEGIAVCDLPEDTMLPGEM

Entity 2 Entity 2 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	106

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1civa1
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	d1civa2
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 (2 domains)

Domain ID domain_id	1civA01
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	1civA02
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

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8. Citations (2)

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Unit-cell length a length_a	147.800 Å
Unit-cell length b length_b	147.800 Å
Unit-cell length c length_c	64.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2050
R_free r_free	0.2840

fit	/app/data/saxs_computation/ci/1civ/1civ.fit
pddf	/app/data/pr_computation/ci/1civ/1civ.pr.out
profile	/app/data/saxs_computation/ci/1civ/1civ.dat

CHLOROPLAST NADP-DEPENDENT MALATE DEHYDROGENASE FROM FLAVERIA BIDENTIS

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

NADP-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