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- PDB-2h63: Crystal Structure of Human Biliverdin Reductase A -

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Basic information

Entry
Database: PDB / ID: 2h63
TitleCrystal Structure of Human Biliverdin Reductase A
ComponentsBiliverdin reductase A
KeywordsOXIDOREDUCTASE / Biliverdin reductase / BLVRA / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


biliverdin reductase / biliverdin reductase [NAD(P)+] activity / : / heme catabolic process / Heme degradation / zinc ion binding / extracellular exosome / cytosol
Similarity search - Function
Biliverdin reductase, catalytic / Biliverdin reductase A / Biliverdin reductase, catalytic / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Biliverdin reductase, catalytic / Biliverdin reductase A / Biliverdin reductase, catalytic / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Biliverdin reductase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKavanagh, K. / Elkins, J. / Ugochukwu, E. / Guo, K. / Pilka, E. / Lukacik, P. / Smee, C. / Papagrigoriou, E. / Bunkoczi, G. / Sundstrom, M. ...Kavanagh, K. / Elkins, J. / Ugochukwu, E. / Guo, K. / Pilka, E. / Lukacik, P. / Smee, C. / Papagrigoriou, E. / Bunkoczi, G. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Biliverdin Reductase A
Authors: Kavanagh, K. / Elkins, J. / Ugochukwu, E. / Guo, K. / Pilka, E. / Lukacik, P. / Smee, C. / Papagrigoriou, E. / Oppermann, U.
History
DepositionMay 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Structure summary / Category: software / struct
Item: _software.classification / _software.name / _struct.title
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biliverdin reductase A
B: Biliverdin reductase A
C: Biliverdin reductase A
D: Biliverdin reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0548
Polymers132,0804
Non-polymers2,9744
Water41423
1
A: Biliverdin reductase A
C: Biliverdin reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5274
Polymers66,0402
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-28 kcal/mol
Surface area23890 Å2
MethodPISA
2
B: Biliverdin reductase A
D: Biliverdin reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5274
Polymers66,0402
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-25 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.787, 92.747, 147.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 2

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETAA6 - 2902 - 286
2ARGARGBB7 - 2903 - 286
3ARGARGCC7 - 2903 - 286
4METMETDD6 - 2902 - 286

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Components

#1: Protein
Biliverdin reductase A / Biliverdin-IX alpha-reductase / BVR A


Mass: 33020.035 Da / Num. of mol.: 4 / Fragment: residues 7-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLVRA / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P53004, biliverdin reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MgCl2, Bis-Tris, PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→41.3 Å / Num. obs: 33769 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.85 Å / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LC0.pdb

1lc0


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.875 / SU B: 36.009 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28691 1399 4.1 %RANDOM
Rwork0.23735 ---
all0.23943 32324 --
obs0.23943 32324 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.219 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--3.73 Å20 Å2
3----3.95 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8453 0 192 23 8668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228818
X-RAY DIFFRACTIONr_bond_other_d0.0020.025814
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.99611965
X-RAY DIFFRACTIONr_angle_other_deg0.9543.00214087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66451123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48623.628328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.771151423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4911544
X-RAY DIFFRACTIONr_chiral_restr0.0810.21398
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029729
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021779
X-RAY DIFFRACTIONr_nbd_refined0.2420.21878
X-RAY DIFFRACTIONr_nbd_other0.1920.25737
X-RAY DIFFRACTIONr_nbtor_refined0.1950.24231
X-RAY DIFFRACTIONr_nbtor_other0.090.24865
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.229
X-RAY DIFFRACTIONr_mcbond_it0.4381.55738
X-RAY DIFFRACTIONr_mcbond_other0.1211.52310
X-RAY DIFFRACTIONr_mcangle_it0.77328853
X-RAY DIFFRACTIONr_scbond_it1.26533493
X-RAY DIFFRACTIONr_scangle_it2.0444.53112
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1638tight positional0.040.05
2B1638tight positional0.040.05
3C1638tight positional0.040.05
4D1638tight positional0.050.05
1A1695medium positional0.230.5
2B1695medium positional0.250.5
3C1695medium positional0.270.5
4D1695medium positional0.250.5
1A1638tight thermal0.080.5
2B1638tight thermal0.070.5
3C1638tight thermal0.070.5
4D1638tight thermal0.080.5
1A1695medium thermal0.462
2B1695medium thermal0.412
3C1695medium thermal0.412
4D1695medium thermal0.442
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 96 -
Rwork0.459 2209 -
obs--90.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
14.0297-1.7986-1.10014.53720.71135.88120.02180.50210.2853-0.4298-0.1036-0.2183-0.2350.03410.0817-0.4384-0.0741-0.0214-0.18420.0943-0.268917.0599.789-19.8899
22.1938-0.7641-0.70766.45030.24116.2777-0.21580.3095-0.5018-0.1308-0.12660.22441.5895-0.37150.3424-0.0221-0.00020.0866-0.1767-0.0889-0.112616.2307-13.5941-15.5491
36.1872-1.035-0.61851.93070.01663.45540.1841-0.8433-0.25580.15050.0606-0.05280.27490.4226-0.2447-0.2752-0.0081-0.198-0.0280.0323-0.1774-17.4004-7.2286-16.9517
45.63660.3584-1.85720.7792-0.37847.46080.1474-0.1208-0.40730.06920.04980.2460.9225-1.0441-0.1971-0.1864-0.0962-0.1455-0.11310.1371-0.0498-40.7713-10.0236-21.4732
54.05581.3496-0.08685.1327-1.16455.0272-0.2905-0.4860.13421.52580.29870.0217-0.68-0.6595-0.00810.30.26820.0545-0.1453-0.0505-0.272626.96793.0317-55.2444
61.7312-0.70650.18274.6812-0.70648.2242-0.1698-0.3841-0.69340.8760.0493-0.10731.2666-0.06450.12050.1845-0.03570.1782-0.1220.1848-0.07927.4762-20.2192-60.0491
73.34830.52091.06023.795-0.6735.14740.14460.3065-0.3398-0.48430.07130.1490.23420.3984-0.2158-0.19670.0049-0.1939-0.2839-0.1245-0.279-30.9877-4.339-55.3043
84.32511.00880.44881.2394-0.5617.0076-0.02160.6458-0.4915-0.29480.0136-0.37640.27471.68810.008-0.2006-0.0118-0.04230.3847-0.16-0.1466-8.0597-1.7067-50.5508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1202 - 116
2X-RAY DIFFRACTION1AA245 - 290241 - 286
3X-RAY DIFFRACTION2AA121 - 244117 - 240
4X-RAY DIFFRACTION3BB7 - 1203 - 116
5X-RAY DIFFRACTION3BB245 - 290241 - 286
6X-RAY DIFFRACTION4BB121 - 244117 - 240
7X-RAY DIFFRACTION5CC7 - 1203 - 116
8X-RAY DIFFRACTION5CC245 - 290241 - 286
9X-RAY DIFFRACTION6CC121 - 244117 - 240
10X-RAY DIFFRACTION7DD6 - 1202 - 116
11X-RAY DIFFRACTION7DD245 - 290241 - 286
12X-RAY DIFFRACTION8DD121 - 244117 - 240

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