PDB-4xap: Crystal structure of aldo-keto reductase from Sinorhizobium melil...

ID or keywords:

Entry

Database: PDB / ID: 4xap

Title

Crystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021

Components

Aldo-keto reductase

Keywords

OXIDOREDUCTASE / PSI-Biology / New York Structural Genomics Research Consortium / aldo-keto reductase / NADP-binding / NYSGRC

Function / homology

Function and homology information

Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding
Similarity search - Function

Biological species

Rhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.21 Å

Authors

Gasiorowska, O.A. / Handing, K.B. / Shabalin, I.G. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021
Authors: Gasiorowska, O.A. / Handing, K.B. / Shabalin, I.G. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

History

Deposition	Dec 15, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 31, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 4, 2015	Group: Derived calculations
Revision 1.2	Oct 14, 2015	Group: Data collection
Revision 1.3	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Apr 13, 2022	Group: Database references / Structure summary / Category: audit_author / citation_author / database_2 Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6	Sep 27, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4xap.cif.gz	123 KB	Display	PDBx/mmCIF format
PDB format	pdb4xap.ent.gz	93.7 KB	Display	PDB format
PDBx/mmJSON format	4xap.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4xap_validation.pdf.gz	418.5 KB	Display	wwPDB validaton report
Full document	4xap_full_validation.pdf.gz	419.1 KB	Display
Data in XML	4xap_validation.xml.gz	12.7 KB	Display
Data in CIF	4xap_validation.cif.gz	17.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xa/4xap ftp://data.pdbj.org/pub/pdb/validation_reports/xa/4xap	HTTPS FTP

-
Related structure data

Related structure data	4pmjS S: Starting model for refinement
Similar structure data	3t0i-1 4j24-3 4pmj-d 4s15-1 5q16-1 5q1h-2 2eyu-1 6cng-1 3qav-d 5iaw-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: NYSGRC-012048

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#92 - Aug 2007 Anabolic Steroids similarity (4)

Deposited unit

A: Aldo-keto reductase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	44.533, 78.068, 79.073
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

biological unit is the same as asym.

#1: Protein	Aldo-keto reductase Mass: 30844.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria) Strain: 1021 / Gene: R02112, SMc01429 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL References: UniProt: Q92NR7, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Aldo-keto reductase

Mass: 30844.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: R02112, SMc01429 / Plasmid: pSGC-His / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q92NR7, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.37 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the PEG/Ion HT condition #70 (0.2M Ammonium Citrate ...Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the PEG/Ion HT condition #70 (0.2M Ammonium Citrate Tribasic anhydrous, 20% w/v PEG 3350 pH=7) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 1 mg/ml TEV solution at 289 K for 1 hour

Crystal

Density Matthews: 2.06 Å³/Da / Density % sol: 40.37 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the PEG/Ion HT condition #70 (0.2M Ammonium Citrate ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.978 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2014 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.978 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. obs: 14216 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / B_iso Wilson estimate: 37.2 Å² / R_merge(I) obs: 0.072 / R_pim(I) all: 0.035 / R_rim(I) all: 0.08 / R_sym value: 0.072 / Χ²: 0.883 / Net I/av σ(I): 20.282 / Net I/σ(I): 17.6 / Num. measured all: 65764

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.2-2.24	4.5	0.692	2.1	694	0.805	0.327	0.768	0.717	98.7
2.24-2.28	4.6	0.595		680	0.853	0.285	0.662	0.783	98.3
2.28-2.32	4.6	0.479		714	0.88	0.227	0.532	0.722	98.6
2.32-2.37	4.6	0.387		676	0.901	0.184	0.43	0.741	97.5
2.37-2.42	4.6	0.379		682	0.887	0.181	0.421	0.77	98
2.42-2.48	4.7	0.354		709	0.926	0.17	0.394	0.788	98.6
2.48-2.54	4.7	0.309		689	0.936	0.147	0.343	0.763	98.9
2.54-2.61	4.6	0.257		702	0.961	0.123	0.286	0.81	98.3
2.61-2.69	4.7	0.208		688	0.969	0.1	0.232	0.837	97.9
2.69-2.77	4.7	0.175		713	0.981	0.085	0.195	0.805	97.8
2.77-2.87	4.7	0.148		691	0.983	0.071	0.164	0.886	98.6
2.87-2.99	4.7	0.128		709	0.985	0.062	0.143	0.95	98.2
2.99-3.12	4.7	0.094		703	0.994	0.046	0.105	0.895	99.2
3.12-3.29	4.7	0.075		719	0.995	0.037	0.084	0.92	99.9
3.29-3.49	4.7	0.059		721	0.997	0.029	0.066	0.979	100
3.49-3.76	4.7	0.048		730	0.998	0.024	0.054	1.071	100
3.76-4.14	4.6	0.04		726	0.998	0.02	0.045	1.048	100
4.14-4.74	4.6	0.033		737	0.998	0.017	0.038	1.04	100
4.74-5.97	4.5	0.031		758	0.999	0.015	0.034	0.799	100
5.97-50	4.3	0.037		775	0.998	0.019	0.042	1.308	95.2

-
Processing

Software

Name	Version	Classification
BLU-MAX		data collection
PDB_EXTRACT	3.15	data extraction
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing
Coot		model building
REFMAC	5.8.0049	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4PMJ

4pmj

Resolution: 2.21→50 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.937 / WR_factor R_free: 0.2053 / WR_factor R_work: 0.146 / FOM work R set: 0.8229 / SU B: 13.137 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2534 / SU R_free: 0.2067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2246	770	5.4 %	RANDOM
R_work	0.1599	13410	-	-
obs	0.1634	13410	98.3 %	-

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 max: 102.16 Å² / B_iso mean: 42.116 Å² / B_iso min: 22.23 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.41 Å²	-0 Å²	0 Å²
2-	-	1.12 Å²	-0 Å²
3-	-	-	0.29 Å²

Refinement step

Cycle: final / Resolution: 2.21→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2119	0	0	103	2222
B_iso mean	-	-	-	44.37	-
Num. residues	-	-	-	-	281

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	2159
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2069
X-RAY DIFFRACTION	r_angle_refined_deg	1.72	1.97	2934
X-RAY DIFFRACTION	r_angle_other_deg	0.855	3	4744
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.894	5	280
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.377	23.404	94
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.546	15	348
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.444	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	333
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	2479
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	475
X-RAY DIFFRACTION	r_mcbond_it	1.507	2.358	1123
X-RAY DIFFRACTION	r_mcbond_other	1.503	2.357	1122
X-RAY DIFFRACTION	r_mcangle_it	2.195	3.531	1402

LS refinement shell

Resolution: 2.207→2.264 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	45	-
R_work	0.246	925	-
all	-	970	-
obs	-	-	92.91 %

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	24.3256	30.172	10.0993	37.553	12.5761	4.2391	-1.3504	1.4046	-1.6033	-1.9509	1.9637	-2.0498	-0.6996	0.6316	-0.6133	0.8383	-0.3727	0.0996	0.57	-0.3064	0.3249	-3.18	14.912	13.562
2	1.7728	-1.9219	1.6719	4.3106	-2.5883	3.6493	0.1048	-0.0091	-0.1166	0.0852	-0.0224	0.0505	-0.0587	0.095	-0.0823	0.1275	0.0084	-0.0076	0.1872	-0.0151	0.1157	-7.405	-2.442	9.308
3	0.3066	-0.3632	-0.5472	1.0586	0.694	2.0406	0.0537	-0.1191	0.0269	0.0995	-0.0918	0.0352	0.0105	0.0076	0.0382	0.2144	-0.0266	-0.0011	0.2139	-0.0308	0.0941	-7.273	-2.89	16.894
4	3.6612	-1.2819	-1.2548	2.5837	0.9025	4.129	0.1458	-0.4132	0.1108	0.3132	0.0441	-0.1756	0.209	0.2253	-0.1898	0.2076	-0.0629	0.0117	0.1923	0.0145	0.0702	-11.949	-10.052	16.661
5	2.2999	1.6009	-0.2725	3.9448	1.7858	2.016	0.0194	-0.0166	-0.0309	0.1394	0.0488	0.1981	0.0814	-0.0841	-0.0682	0.1515	0.0051	-0.0044	0.1751	0.0497	0.1028	-16.078	-12.936	4.667
6	0.8714	0.0123	-0.3858	1.4648	1.0755	2.3929	0.0055	0.0054	-0.1974	-0.028	-0.0734	0.3015	-0.0042	-0.0918	0.068	0.1524	-0.0112	-0.004	0.1844	0.0054	0.1515	-15.566	-13.641	4.157
7	1.8228	0.3217	-0.0679	1.0338	-0.2099	0.1626	-0.0064	0.0314	-0.0131	-0.1446	0.0188	0.0481	0.046	0.0284	-0.0123	0.1581	0.0135	-0.0086	0.2074	-0.0035	0.0772	-10.853	-6.872	-5.884
8	2.6695	0.0437	1.4045	1.0613	-0.1803	1.1897	0.0661	-0.0131	-0.0099	-0.021	-0.0557	-0.1735	-0.0204	0.1058	-0.0104	0.1465	-0.0053	0.0059	0.201	0.0125	0.121	4.725	2.583	3.859
9	2.8294	1.1034	-4.5522	7.978	-6.325	10.0825	-0.0159	-0.2694	0.0284	0.2513	-0.1207	-0.2466	-0.0962	0.4511	0.1366	0.1892	-0.0289	-0.0216	0.2121	-0.037	0.1346	1.662	5.92	15.881
10	1.1287	0.6019	1.7961	7.5225	3.0147	5.4425	-0.0778	0.1836	0.1268	-0.4229	0.0669	-0.2375	-0.5058	0.4278	0.0109	0.1182	-0.0589	0.0609	0.2346	0.0638	0.2205	12.567	10.139	-1.906
11	5.3646	1.5229	-5.2177	3.2592	0.4084	6.4182	-0.2564	-0.3432	-0.5167	-0.2153	-0.1206	-0.4244	0.2628	0.384	0.377	0.2141	0.0681	0.0711	0.347	0.0544	0.1866	5.586	-7.616	-9.768

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 5
2	X-RAY DIFFRACTION	2	A	6 - 32
3	X-RAY DIFFRACTION	3	A	33 - 55
4	X-RAY DIFFRACTION	4	A	56 - 74
5	X-RAY DIFFRACTION	5	A	75 - 97
6	X-RAY DIFFRACTION	6	A	98 - 122
7	X-RAY DIFFRACTION	7	A	123 - 183
8	X-RAY DIFFRACTION	8	A	184 - 240
9	X-RAY DIFFRACTION	9	A	241 - 255
10	X-RAY DIFFRACTION	10	A	256 - 271
11	X-RAY DIFFRACTION	11	A	272 - 281

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi