4INF | pdb_00004inf

Crystal structure of amidohydrolase saro_0799 (target efi-505250) from novosphingobium aromaticivorans dsm 12444 with bound calcium

PDB DOI: https://doi.org/10.2210/pdb4INF/pdb

Classification: HYDROLASE
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-01-04 Released: 2013-01-16
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.190 (Depositor), 0.184 (DCC)
R-Value Work:
0.141 (Depositor)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of amidohydrolase sarp_0799 (target efi-505250) from novosphingobium aromaticivorans

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 171 kDa
Atom Count: 13,452
Modeled Residue Count: 1,396
Deposited Residue Count: 1,492
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METAL-DEPENDENT HYDROLASE	A, B, C, D	373	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0 Gene Names: Saro_0799
UniProt
Find proteins for Q2GA79 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2GA79 Go to UniProtKB: Q2GA79
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2GA79
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
OXD Query on OXD Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain S [auth B] SDF format, chain K [auth A] SDF format, chain CA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth D]	CA [auth D], K [auth A], S [auth B], Y [auth C]	OXALIC ACID C₂ H₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain K [auth A] Focus chain S [auth B] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain K [auth A] Focus chain S [auth B] Focus chain Y [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain T [auth C] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth C] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth C] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B], T [auth C], Z [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] F [auth A] G [auth A] H [auth A] AA [auth D], BA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.190 (Depositor), 0.184 (DCC)
R-Value Work: 0.141 (Depositor)
R-Value Observed: 0.143 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.945	α = 90
b = 61.024	β = 103.35
c = 131.385	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-01-16

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-01-16
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description