HEADER OXYGEN BINDING 26-APR-22 7ZOS TITLE CLASS 1 PHYTOGLOBIN FROM SUGAR BEET (BVPGB1.2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-SYMBIOTIC HEMOGLOBIN CLASS 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BVPGB1.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BETA VULGARIS; SOURCE 3 ORGANISM_TAXID: 161934; SOURCE 4 GENE: BV9_224250_AAYD.T2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PLANT HEMOGLOBIN, PHYTOGLOBIN, NITROGEN METABOLISM, REDOX BALANCE, KEYWDS 2 OXYGEN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.NYBLOM,S.CHRISTENSEN,N.ERIKSSON,L.BULOW REVDAT 3 07-FEB-24 7ZOS 1 REMARK REVDAT 2 01-MAR-23 7ZOS 1 REMARK LINK REVDAT 1 07-SEP-22 7ZOS 0 JRNL AUTH S.CHRISTENSEN,L.GROTH,N.LEIVA-ERIKSSON,M.NYBLOM,L.BULOW JRNL TITL OXIDATIVE IMPLICATIONS OF SUBSTITUTING A CONSERVED CYSTEINE JRNL TITL 2 RESIDUE IN SUGAR BEET PHYTOGLOBIN BVPGB 1.2. JRNL REF ANTIOXIDANTS V. 11 2022 JRNL REFN ESSN 2076-3921 JRNL PMID 36009334 JRNL DOI 10.3390/ANTIOX11081615 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18440 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.250 REMARK 3 FREE R VALUE TEST SET COUNT : 969 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 47.9000 - 3.6400 1.00 2660 154 0.1797 0.2197 REMARK 3 2 3.6400 - 2.8900 1.00 2503 150 0.2227 0.2334 REMARK 3 3 2.8900 - 2.5200 1.00 2501 121 0.2112 0.2327 REMARK 3 4 2.5200 - 2.2900 1.00 2460 144 0.2120 0.2796 REMARK 3 5 2.2900 - 2.1300 1.00 2463 134 0.2093 0.2451 REMARK 3 6 2.1300 - 2.0000 1.00 2441 130 0.2306 0.2668 REMARK 3 7 2.0000 - 1.9000 1.00 2443 136 0.2563 0.2922 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) : 0.163 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.244 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.94 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 : 0.011 1232 REMARK 3 ANGLE : 1.465 1669 REMARK 3 CHIRALITY : 0.057 178 REMARK 3 PLANARITY : 0.007 198 REMARK 3 DIHEDRAL : 5.994 716 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 7ZOS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292120708. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18443 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 68.413 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 25.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3ZHW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG6000, 0.1 M CITRATE, PH REMARK 280 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.37500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.37500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.37500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.37500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.37500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.37500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.37500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 -7 REMARK 465 SER A -6 REMARK 465 PHE A -5 REMARK 465 THR A -4 REMARK 465 ASN A -3 REMARK 465 VAL A -2 REMARK 465 ASN A -1 REMARK 465 TYR A 0 REMARK 465 PRO A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 ASP A 4 REMARK 465 GLY A 5 REMARK 465 PHE A 52 REMARK 465 VAL A 53 REMARK 465 ARG A 54 REMARK 465 ASP A 55 REMARK 465 SER A 56 REMARK 465 ASP A 57 REMARK 465 VAL A 58 REMARK 465 PRO A 59 REMARK 465 LEU A 60 REMARK 465 GLU A 61 REMARK 465 GLN A 62 REMARK 465 GLN A 162 REMARK 465 PRO A 163 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 78 N CYN A 202 1.63 REMARK 500 SG CYS A 78 C CYN A 202 1.69 REMARK 500 SD MET A 76 C21 FC6 A 203 1.73 REMARK 500 SD MET A 76 N25 FC6 A 203 1.83 REMARK 500 CB CYS A 78 N CYN A 202 2.09 REMARK 500 OE2 GLU A 143 O HOH A 301 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 69 NE2 REMARK 620 2 HEM A 201 NA 94.2 REMARK 620 3 HEM A 201 NB 91.4 86.6 REMARK 620 4 HEM A 201 NC 84.6 178.6 94.2 REMARK 620 5 HEM A 201 ND 85.7 93.3 177.1 85.8 REMARK 620 6 HIS A 104 NE2 173.7 92.0 90.1 89.2 92.8 REMARK 620 N 1 2 3 4 5 DBREF 7ZOS A -7 163 UNP V5QR23 V5QR23_BETVV 1 171 SEQRES 1 A 171 MET SER PHE THR ASN VAL ASN TYR PRO ALA SER ASP GLY SEQRES 2 A 171 THR VAL ILE PHE THR GLU GLU GLN GLU ALA LEU VAL VAL SEQRES 3 A 171 GLN SER TRP ASN VAL MET LYS LYS ASN SER ALA GLU LEU SEQRES 4 A 171 GLY LEU LYS LEU PHE LEU LYS ILE PHE GLU ILE ALA PRO SEQRES 5 A 171 THR ALA LYS LYS MET PHE SER PHE VAL ARG ASP SER ASP SEQRES 6 A 171 VAL PRO LEU GLU GLN ASN GLN LYS LEU LYS GLY HIS ALA SEQRES 7 A 171 MET SER VAL PHE VAL MET THR CYS LYS SER ALA ALA GLN SEQRES 8 A 171 LEU ARG LYS ALA GLY LYS VAL THR PHE GLY GLU SER SER SEQRES 9 A 171 LEU LYS HIS MET GLY SER VAL HIS LEU LYS TYR GLY VAL SEQRES 10 A 171 VAL ASP GLU HIS PHE GLU VAL THR ARG PHE ALA LEU LEU SEQRES 11 A 171 GLU THR ILE LYS GLU ALA VAL PRO GLU MET TRP SER PRO SEQRES 12 A 171 GLU MET LYS ASN ALA TRP ALA GLU ALA PHE ASN HIS LEU SEQRES 13 A 171 VAL ALA ALA ILE LYS ALA GLU MET GLN ARG LEU SER THR SEQRES 14 A 171 GLN PRO HET HEM A 201 43 HET CYN A 202 2 HET FC6 A 203 13 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CYN CYANIDE ION HETNAM FC6 HEXACYANOFERRATE(3-) HETSYN HEM HEME HETSYN FC6 FERRI(III)HEXACYANIDE FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CYN C N 1- FORMUL 4 FC6 C6 FE N6 FORMUL 5 HOH *95(H2 O) HELIX 1 AA1 THR A 10 LYS A 25 1 16 HELIX 2 AA2 ASN A 27 ALA A 43 1 17 HELIX 3 AA3 PRO A 44 SER A 51 5 8 HELIX 4 AA4 GLN A 64 GLY A 88 1 25 HELIX 5 AA5 GLY A 93 GLY A 108 1 16 HELIX 6 AA6 VAL A 110 VAL A 129 1 20 HELIX 7 AA7 SER A 134 THR A 161 1 28 LINK NE2 HIS A 69 FE HEM A 201 1555 1555 2.05 LINK NE2 HIS A 104 FE HEM A 201 1555 1555 2.07 CRYST1 96.750 96.750 47.900 90.00 90.00 90.00 P 4 21 2 8 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 0.010336 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020877 0.00000