3RED | pdb_00003red

3.0 A structure of the Prunus mume hydroxynitrile lyase isozyme-1

PDB DOI: https://doi.org/10.2210/pdb3RED/pdb

Classification: LYASE
Organism(s): Prunus mume
Mutation(s): No

Deposited: 2011-04-04 Released: 2012-06-20
Deposition Author(s): Cielo, C.B.C., Yamane, T., Asano, Y., Watanabe, N., Suzuki, A., Fukuta, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free:
0.253 (Depositor), 0.250 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of a native FAD-dependent Hydroxynitrile Lyase derived from the Japanese apricot, Prunus mume

Cielo, C.B.C., Yamane, T., Asano, Y., Watanabe, N., Suzuki, A., Fukuta, Y.

To be published.

Macromolecule Content

Total Structure Weight: 686.4 kDa
Atom Count: 48,604
Modeled Residue Count: 6,252
Deposited Residue Count: 6,252
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxynitrile lyase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	521	Prunus mume	Mutation(s): 0 EC: 4.1.2.10
UniProt
Find proteins for B9X0I1 (Prunus mume) Explore B9X0I1 Go to UniProtKB: B9X0I1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9X0I1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain S [auth G] SDF format, chain T [auth H] SDF format, chain U [auth I] SDF format, chain V [auth J] SDF format, chain W [auth K] SDF format, chain X [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] MOL2 format, chain V [auth J] MOL2 format, chain W [auth K] MOL2 format, chain X [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H] mmCIF format, chain U [auth I] mmCIF format, chain V [auth J] mmCIF format, chain W [auth K] mmCIF format, chain X [auth L]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free: 0.253 (Depositor), 0.250 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.019	α = 89.92
b = 113.302	β = 79.13
c = 169.488	γ = 80.83

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-06-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-20
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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3.0 A structure of the Prunus mume hydroxynitrile lyase isozyme-1

Crystal Structure of a native FAD-dependent Hydroxynitrile Lyase derived from the Japanese apricot, Prunus mume

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations