PDB-9ldp: Zn-Carbonic Anhydrase II soaked with 3NT under 15 atm CO2

ID or keywords:

Entry

Database: PDB / ID: 9ldp

Title

Zn-Carbonic Anhydrase II soaked with 3NT under 15 atm CO2

Components

Carbonic anhydrase 2

Keywords

METAL BINDING PROTEIN / Carbonic Anhydrase / enzyme mechanism / metalloenzymes

Function / homology

Function and homology information

positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.14 Å

Authors

Kim, C.U. / Kim, J.K.

Funding support

Korea, Republic Of, 1items

Citation

Journal: To Be Published
Title: Temperature series of human Carbonic Anhydrase II with photolysis of caged CO2
Authors: Kim, C.U. / Kim, J.K.

History

Deposition	Jan 6, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ldp.cif.gz	167.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9ldp.ent.gz	99.7 KB	Display	PDB format
PDBx/mmJSON format	9ldp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ldp_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9ldp_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9ldp_validation.xml.gz	16.7 KB	Display
Data in CIF	9ldp_validation.cif.gz	23.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ld/9ldp ftp://data.pdbj.org/pub/pdb/validation_reports/ld/9ldp	HTTPS FTP

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Related structure data

Related structure data	7y2aC 7y2cC 7y2eC 7y2fC 7y2gC 7y2hC 7y2iC 7y2jC 7y2kC 7y2lC 7y2mC 7y2nC 7y2oC 7y2qC 7y2rC 7y2sC 7y2tC 7y2uC 7y2vC 7y2wC 7y2xC 8wepC 8werC 8wesC 9l2xC 9l2yC 9l2zC 9l30C 9l31C 9l32C 9l33C 9ldoC 9lr6C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#49 - Jan 2004 Carbonic Anhydrase similarity (2) #222 - Jun 2018 Proteins and Nanoparticles similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: Carbonic anhydrase 2

hetero molecules

29.4 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)	41.787, 41.202, 71.952
Angle α, β, γ (deg.)	90.000, 104.082, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II Mass: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CO2 / CARBON DIOXIDE Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 40.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3 M sodium citrate, 50 mM Tris-HCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.8856 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 14, 2019
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8856 Å / Relative weight: 1
Reflection	Resolution: 1.14→30 Å / Num. obs: 85689 / % possible obs: 98.8 % / Redundancy: 6.3 % / CC_1/2: 0.998 / CC star: 0.999 / R_merge(I) obs: 0.054 / R_pim(I) all: 0.022 / R_rim(I) all: 0.058 / Net I/σ(I): 34.8
Reflection shell	Resolution: 1.14→1.16 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.378 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4251 / CC_1/2: 0.903 / CC star: 0.974 / R_pim(I) all: 0.16 / R_rim(I) all: 0.412 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
HKL-2000		data reduction
HKL-2000		data scaling
REFMAC	5.8.0430	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.14→28.911 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.963 / SU B: 1.046 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.175	4178	4.878 %
R_work	0.1524	81468	-
all	0.153	-	-
obs	-	85646	98.759 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 12.087 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.323 Å²	0 Å²	-0.081 Å²
2-	-	-0.227 Å²	0 Å²
3-	-	-	-0.049 Å²

Refinement step

Cycle: LAST / Resolution: 1.14→28.911 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2049	0	7	248	2304

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	2227
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2041
X-RAY DIFFRACTION	r_angle_refined_deg	2.062	1.817	3045
X-RAY DIFFRACTION	r_angle_other_deg	0.73	1.781	4755
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.884	5	286
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.661	5	7
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.853	10	373
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.786	10	105
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	317
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	2668
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	499
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	457
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	1952
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	1069
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.091	0.2	1107
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.225	0.2	170
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.12	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.072	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.273	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.274	0.2	93
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.157	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	5.138	1.154	1084
X-RAY DIFFRACTION	r_mcbond_other	5.109	1.153	1084
X-RAY DIFFRACTION	r_mcangle_it	7.418	2.079	1372
X-RAY DIFFRACTION	r_mcangle_other	7.419	2.08	1373
X-RAY DIFFRACTION	r_scbond_it	5.953	1.322	1143
X-RAY DIFFRACTION	r_scbond_other	5.931	1.322	1140
X-RAY DIFFRACTION	r_scangle_it	8.413	2.317	1667
X-RAY DIFFRACTION	r_scangle_other	8.394	2.318	1666
X-RAY DIFFRACTION	r_lrange_it	15.937	14.576	2596
X-RAY DIFFRACTION	r_lrange_other	14.707	13.694	2534
X-RAY DIFFRACTION	r_rigid_bond_restr	4.33	3	4268

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.14-1.17	0.22	324	0.204	5936	0.205	6354	0.974	0.979	98.5206	0.174
1.17-1.202	0.195	307	0.179	5849	0.179	6243	0.978	0.981	98.6064	0.149
1.202-1.236	0.185	311	0.161	5589	0.162	6002	0.977	0.983	98.3006	0.135
1.236-1.274	0.183	285	0.151	5490	0.153	5894	0.977	0.984	97.981	0.128
1.274-1.316	0.166	316	0.137	5249	0.138	5674	0.983	0.988	98.079	0.117
1.316-1.362	0.172	263	0.132	5150	0.134	5525	0.981	0.989	97.9729	0.113
1.362-1.413	0.166	219	0.137	4998	0.139	5301	0.981	0.988	98.4154	0.118
1.413-1.471	0.159	251	0.126	4798	0.128	5113	0.984	0.99	98.7483	0.11
1.471-1.536	0.171	242	0.131	4651	0.133	4930	0.98	0.989	99.2495	0.117
1.536-1.611	0.159	231	0.125	4420	0.126	4679	0.985	0.991	99.4016	0.115
1.611-1.698	0.166	201	0.126	4245	0.128	4460	0.983	0.99	99.6861	0.118
1.698-1.8	0.154	213	0.134	4039	0.135	4268	0.985	0.989	99.6251	0.13
1.8-1.924	0.168	207	0.138	3750	0.139	3968	0.984	0.988	99.7228	0.139
1.924-2.078	0.166	170	0.144	3547	0.145	3733	0.982	0.988	99.5714	0.151
2.078-2.275	0.156	170	0.147	3253	0.147	3430	0.986	0.987	99.7959	0.157
2.275-2.541	0.18	143	0.161	2944	0.162	3098	0.978	0.984	99.6449	0.177
2.541-2.931	0.194	107	0.176	2660	0.177	2769	0.98	0.98	99.9278	0.201
2.931-3.58	0.193	88	0.173	2252	0.174	2340	0.973	0.981	100	0.205
3.58-5.025	0.184	74	0.154	1752	0.155	1829	0.983	0.988	99.836	0.19
5.025-28.911	0.184	56	0.208	881	0.206	1084	0.98	0.978	86.4391	0.252

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