HEADER OXIDOREDUCTASE 26-SEP-22 8ELM TITLE APO HUMAN BILIVERDIN REDUCTASE BETA (293K) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVIN REDUCTASE (NADPH); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FR,BILIVERDIN REDUCTASE B,BVR-B,BILIVERDIN-IX BETA- COMPND 5 REDUCTASE,GREEN HEME-BINDING PROTEIN,GHBP,NADPH-DEPENDENT DIAPHORASE, COMPND 6 NADPH-FLAVIN REDUCTASE,FLR; COMPND 7 EC: 1.5.1.30,1.3.1.24; COMPND 8 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: BLVRB, FLR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS APO, ROOM-TEMPERATURE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.MCLEOD,E.Z.EISENMESSER,E.LEE,R.E.THORNE REVDAT 2 13-SEP-23 8ELM 1 JRNL REVDAT 1 06-SEP-23 8ELM 0 JRNL AUTH E.LEE,M.J.MCLEOD,J.S.REDZIC,B.MARCOLIN,R.E.THORNE,P.AGARWAL, JRNL AUTH 2 E.Z.EISENMESSER JRNL TITL IDENTIFYING STRUCTURAL AND DYNAMIC CHANGES DURING THE JRNL TITL 2 BILIVERDIN REDUCTASE B CATALYTIC CYCLE. JRNL REF FRONT MOL BIOSCI V. 10 44587 2023 JRNL REFN ESSN 2296-889X JRNL PMID 37645217 JRNL DOI 10.3389/FMOLB.2023.1244587 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 10970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 545 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 50.5000 - 3.4700 1.00 2751 130 0.1631 0.2164 REMARK 3 2 3.4700 - 2.7600 1.00 2615 137 0.1869 0.2390 REMARK 3 3 2.7600 - 2.4100 0.99 2568 143 0.1882 0.2239 REMARK 3 4 2.4100 - 2.1900 0.98 2491 135 0.1879 0.2394 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.214 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.557 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.67 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 : 0.002 1626 REMARK 3 ANGLE : 0.423 2223 REMARK 3 CHIRALITY : 0.043 262 REMARK 3 PLANARITY : 0.003 290 REMARK 3 DIHEDRAL : 9.757 596 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.9026 -7.6607 -15.0774 REMARK 3 T TENSOR REMARK 3 T11: 0.2207 T22: 0.1701 REMARK 3 T33: 0.2447 T12: -0.0285 REMARK 3 T13: -0.0241 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 3.6600 L22: 4.1770 REMARK 3 L33: 4.5975 L12: -0.7209 REMARK 3 L13: 0.9860 L23: 0.7260 REMARK 3 S TENSOR REMARK 3 S11: 0.0969 S12: -0.1035 S13: -0.3524 REMARK 3 S21: 0.2220 S22: 0.0152 S23: 0.1101 REMARK 3 S31: 0.3797 S32: -0.0765 S33: -0.0996 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.1128 7.4930 -19.5120 REMARK 3 T TENSOR REMARK 3 T11: 0.2552 T22: 0.2883 REMARK 3 T33: 0.3203 T12: 0.0091 REMARK 3 T13: -0.0094 T23: 0.0282 REMARK 3 L TENSOR REMARK 3 L11: 2.5469 L22: 0.3974 REMARK 3 L33: 1.5233 L12: 0.8051 REMARK 3 L13: -0.2715 L23: 0.3728 REMARK 3 S TENSOR REMARK 3 S11: -0.0277 S12: 0.4521 S13: 0.2441 REMARK 3 S21: -0.0676 S22: 0.0911 S23: -0.1129 REMARK 3 S31: -0.0109 S32: 0.1388 S33: -0.0031 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 143 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.5280 3.7031 -3.5175 REMARK 3 T TENSOR REMARK 3 T11: 0.2659 T22: 0.2681 REMARK 3 T33: 0.2415 T12: -0.0059 REMARK 3 T13: -0.0300 T23: -0.0362 REMARK 3 L TENSOR REMARK 3 L11: 4.5508 L22: 4.8311 REMARK 3 L33: 4.6660 L12: -0.4343 REMARK 3 L13: 0.8974 L23: -0.3913 REMARK 3 S TENSOR REMARK 3 S11: -0.0322 S12: -0.3832 S13: -0.0363 REMARK 3 S21: 0.1950 S22: 0.1023 S23: -0.3726 REMARK 3 S31: 0.3136 S32: 0.2828 S33: -0.0542 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 8ELM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1000268621. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : 7B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96860 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10970 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 50.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.22800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 1.29600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.810 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6OPL REMARK 200 REMARK 200 REMARK: THIN NEEDLES. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 6.5, 1-4% PEG 20000. REMARK 280 EQUILIBRATED OVER 0.25-0.5 M NACL. BLVRB 18 MG/ML., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 21.29550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.53750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.65450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.53750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.29550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.65450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 MET A 1 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 ARG A 78 44.49 38.55 REMARK 500 THR A 110 -105.40 -113.67 REMARK 500 PRO A 152 -141.16 -79.61 REMARK 500 PRO A 152 -141.50 -79.61 REMARK 500 REMARK 500 REMARK: NULL DBREF 8ELM A 1 206 UNP P30043 BLVRB_HUMAN 1 206 SEQRES 1 A 206 MET ALA VAL LYS LYS ILE ALA ILE PHE GLY ALA THR GLY SEQRES 2 A 206 GLN THR GLY LEU THR THR LEU ALA GLN ALA VAL GLN ALA SEQRES 3 A 206 GLY TYR GLU VAL THR VAL LEU VAL ARG ASP SER SER ARG SEQRES 4 A 206 LEU PRO SER GLU GLY PRO ARG PRO ALA HIS VAL VAL VAL SEQRES 5 A 206 GLY ASP VAL LEU GLN ALA ALA ASP VAL ASP LYS THR VAL SEQRES 6 A 206 ALA GLY GLN ASP ALA VAL ILE VAL LEU LEU GLY THR ARG SEQRES 7 A 206 ASN ASP LEU SER PRO THR THR VAL MET SER GLU GLY ALA SEQRES 8 A 206 ARG ASN ILE VAL ALA ALA MET LYS ALA HIS GLY VAL ASP SEQRES 9 A 206 LYS VAL VAL ALA CYS THR SER ALA PHE LEU LEU TRP ASP SEQRES 10 A 206 PRO THR LYS VAL PRO PRO ARG LEU GLN ALA VAL THR ASP SEQRES 11 A 206 ASP HIS ILE ARG MET HIS LYS VAL LEU ARG GLU SER GLY SEQRES 12 A 206 LEU LYS TYR VAL ALA VAL MET PRO PRO HIS ILE GLY ASP SEQRES 13 A 206 GLN PRO LEU THR GLY ALA TYR THR VAL THR LEU ASP GLY SEQRES 14 A 206 ARG GLY PRO SER ARG VAL ILE SER LYS HIS ASP LEU GLY SEQRES 15 A 206 HIS PHE MET LEU ARG CYS LEU THR THR ASP GLU TYR ASP SEQRES 16 A 206 GLY HIS SER THR TYR PRO SER HIS GLN TYR GLN HET NA A 301 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *49(H2 O) HELIX 1 AA1 GLY A 13 ALA A 26 1 14 HELIX 2 AA2 ASP A 36 LEU A 40 5 5 HELIX 3 AA3 GLN A 57 ALA A 66 1 10 HELIX 4 AA4 THR A 85 GLY A 102 1 18 HELIX 5 AA5 SER A 111 TRP A 116 5 6 HELIX 6 AA6 ASP A 117 VAL A 121 5 5 HELIX 7 AA7 PRO A 122 ARG A 124 5 3 HELIX 8 AA8 LEU A 125 GLU A 141 1 17 HELIX 9 AA9 LYS A 178 CYS A 188 1 11 SHEET 1 AA1 8 HIS A 49 VAL A 52 0 SHEET 2 AA1 8 GLU A 29 VAL A 34 1 N VAL A 32 O VAL A 51 SHEET 3 AA1 8 LYS A 5 PHE A 9 1 N ILE A 8 O THR A 31 SHEET 4 AA1 8 ALA A 70 VAL A 73 1 O ILE A 72 N PHE A 9 SHEET 5 AA1 8 LYS A 105 CYS A 109 1 O VAL A 107 N VAL A 71 SHEET 6 AA1 8 LYS A 145 VAL A 149 1 O VAL A 149 N ALA A 108 SHEET 7 AA1 8 SER A 198 SER A 202 1 O THR A 199 N ALA A 148 SHEET 8 AA1 8 THR A 164 LEU A 167 -1 N THR A 164 O SER A 202 SHEET 1 AA2 2 HIS A 153 GLY A 155 0 SHEET 2 AA2 2 VAL A 175 SER A 177 1 O ILE A 176 N HIS A 153 LINK OG1 THR A 12 NA NA A 301 1555 1555 3.03 CRYST1 42.591 47.309 101.075 90.00 90.00 90.00 P 21 21 21 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 0.023479 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021138 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009894 0.00000