HEADER FLAVOPROTEIN 10-JAN-22 7THG TITLE CRYSTAL STRUCTURE OF HUMAN NADH-CYTOCHROME B5 REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADH-CYTOCHROME B5 REDUCTASE 3 SOLUBLE FORM; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CYB5R3, DIA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FAD, B5R, REDUCTASE, NADH, FLAVOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.ZHENG,P.H.THIBODEAU REVDAT 2 25-OCT-23 7THG 1 REMARK REVDAT 1 12-APR-23 7THG 0 JRNL AUTH A.ZHENG,P.H.THIBODEAU JRNL TITL STRUCTURE OF WILD-TYPE HUMAN NADH-CYTOCHROME B5 REDUCTASE JRNL TITL 2 AND MUTANTS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 6462 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 645 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.4100 - 4.9600 1.00 1210 142 0.2046 0.2228 REMARK 3 2 4.9500 - 3.9400 0.99 1181 127 0.1987 0.2136 REMARK 3 3 3.9400 - 3.4400 0.98 1139 130 0.2666 0.3368 REMARK 3 4 3.4400 - 3.1300 0.98 1172 121 0.3150 0.3404 REMARK 3 5 3.1200 - 2.9000 0.96 1115 125 0.4281 0.4595 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.454 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.524 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2276 REMARK 3 ANGLE : 1.242 3100 REMARK 3 CHIRALITY : 0.080 333 REMARK 3 PLANARITY : 0.009 396 REMARK 3 DIHEDRAL : 14.408 857 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7THG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000257462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541780 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6909 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 49.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.03 REMARK 200 R MERGE FOR SHELL (I) : 1.20700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1UMK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4K 30%, 0.1M NA/K PO4 PH 7.6, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.55000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.77500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.32500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 27 REMARK 465 ARG A 28 REMARK 465 SER A 29 REMARK 465 THR A 30 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 125 -64.07 -101.91 REMARK 500 TYR A 247 -133.94 -103.26 REMARK 500 CYS A 283 -72.39 -95.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 7THG A 27 300 UNP P00387 NB5R3_HUMAN 28 301 SEQRES 1 A 274 GLN ARG SER THR PRO ALA ILE THR LEU GLU SER PRO ASP SEQRES 2 A 274 ILE LYS TYR PRO LEU ARG LEU ILE ASP ARG GLU ILE ILE SEQRES 3 A 274 SER HIS ASP THR ARG ARG PHE ARG PHE ALA LEU PRO SER SEQRES 4 A 274 PRO GLN HIS ILE LEU GLY LEU PRO VAL GLY GLN HIS ILE SEQRES 5 A 274 TYR LEU SER ALA ARG ILE ASP GLY ASN LEU VAL VAL ARG SEQRES 6 A 274 PRO TYR THR PRO ILE SER SER ASP ASP ASP LYS GLY PHE SEQRES 7 A 274 VAL ASP LEU VAL ILE LYS VAL TYR PHE LYS ASP THR HIS SEQRES 8 A 274 PRO LYS PHE PRO ALA GLY GLY LYS MET SER GLN TYR LEU SEQRES 9 A 274 GLU SER MET GLN ILE GLY ASP THR ILE GLU PHE ARG GLY SEQRES 10 A 274 PRO SER GLY LEU LEU VAL TYR GLN GLY LYS GLY LYS PHE SEQRES 11 A 274 ALA ILE ARG PRO ASP LYS LYS SER ASN PRO ILE ILE ARG SEQRES 12 A 274 THR VAL LYS SER VAL GLY MET ILE ALA GLY GLY THR GLY SEQRES 13 A 274 ILE THR PRO MET LEU GLN VAL ILE ARG ALA ILE MET LYS SEQRES 14 A 274 ASP PRO ASP ASP HIS THR VAL CYS HIS LEU LEU PHE ALA SEQRES 15 A 274 ASN GLN THR GLU LYS ASP ILE LEU LEU ARG PRO GLU LEU SEQRES 16 A 274 GLU GLU LEU ARG ASN LYS HIS SER ALA ARG PHE LYS LEU SEQRES 17 A 274 TRP TYR THR LEU ASP ARG ALA PRO GLU ALA TRP ASP TYR SEQRES 18 A 274 GLY GLN GLY PHE VAL ASN GLU GLU MET ILE ARG ASP HIS SEQRES 19 A 274 LEU PRO PRO PRO GLU GLU GLU PRO LEU VAL LEU MET CYS SEQRES 20 A 274 GLY PRO PRO PRO MET ILE GLN TYR ALA CYS LEU PRO ASN SEQRES 21 A 274 LEU ASP HIS VAL GLY HIS PRO THR GLU ARG CYS PHE VAL SEQRES 22 A 274 PHE HET FAD A1301 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 FAD C27 H33 N9 O15 P2 HELIX 1 AA1 LYS A 125 MET A 133 1 9 HELIX 2 AA2 GLY A 182 ASP A 196 1 15 HELIX 3 AA3 THR A 211 ILE A 215 5 5 HELIX 4 AA4 LEU A 217 HIS A 228 1 12 HELIX 5 AA5 ASN A 253 HIS A 260 1 8 HELIX 6 AA6 PRO A 263 GLU A 267 5 5 HELIX 7 AA7 PRO A 275 ALA A 282 1 8 HELIX 8 AA8 CYS A 283 GLY A 291 1 9 HELIX 9 AA9 PRO A 293 GLU A 295 5 3 SHEET 1 AA1 2 ALA A 32 ILE A 33 0 SHEET 2 AA1 2 HIS A 68 ILE A 69 1 O ILE A 69 N ALA A 32 SHEET 1 AA2 6 ASN A 87 TYR A 93 0 SHEET 2 AA2 6 HIS A 77 ILE A 84 -1 N ILE A 78 O TYR A 93 SHEET 3 AA2 6 THR A 138 SER A 145 -1 O SER A 145 N HIS A 77 SHEET 4 AA2 6 TYR A 42 GLU A 50 -1 N TYR A 42 O PHE A 141 SHEET 5 AA2 6 THR A 56 ALA A 62 -1 O ARG A 58 N GLU A 50 SHEET 6 AA2 6 PHE A 104 LYS A 110 -1 O LEU A 107 N PHE A 59 SHEET 1 AA3 3 LEU A 148 GLY A 152 0 SHEET 2 AA3 3 LYS A 155 ILE A 158 -1 O LYS A 155 N GLN A 151 SHEET 3 AA3 3 ILE A 167 THR A 170 -1 O ILE A 167 N ILE A 158 SHEET 1 AA4 6 GLY A 248 GLN A 249 0 SHEET 2 AA4 6 PHE A 232 LEU A 238 1 N TYR A 236 O GLY A 248 SHEET 3 AA4 6 VAL A 202 ASN A 209 1 N CYS A 203 O LYS A 233 SHEET 4 AA4 6 SER A 173 GLY A 179 1 N ALA A 178 O ALA A 208 SHEET 5 AA4 6 LEU A 269 CYS A 273 1 O LEU A 271 N GLY A 175 SHEET 6 AA4 6 CYS A 297 VAL A 299 1 O PHE A 298 N VAL A 270 CISPEP 1 GLY A 143 PRO A 144 0 -0.57 CRYST1 64.830 64.830 71.100 90.00 90.00 90.00 P 41 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015425 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014065 0.00000