HEADER OXIDOREDUCTASE 14-OCT-20 7AOJ TITLE PLASMOREDOXIN, A REDOX-ACTIVE PROTEIN UNIQUE FOR MALARIA PARASITES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM (ISOLATE 3D7); SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: ISOLATE 3D7; SOURCE 5 GENE: PF3D7_0303600; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MALARIA, PLASMODIUM FALCIPARUM, THIOREDOXIN SUPERFAMILY, REDOX KEYWDS 2 METABOLISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.FRITZ-WOLF,J.BATHKE,S.RAHLFS,K.BECKER REVDAT 3 19-JUN-24 7AOJ 1 REMARK REVDAT 2 27-APR-22 7AOJ 1 JRNL REVDAT 1 13-APR-22 7AOJ 0 JRNL AUTH K.FRITZ-WOLF,J.BATHKE,S.RAHLFS,K.BECKER JRNL TITL CRYSTAL STRUCTURE OF PLASMOREDOXIN, A REDOX-ACTIVE PROTEIN JRNL TITL 2 UNIQUE FOR MALARIA PARASITES. JRNL REF CURR RES STRUCT BIOL V. 4 87 2022 JRNL REFN ESSN 2665-928X JRNL PMID 35434650 JRNL DOI 10.1016/J.CRSTBI.2022.03.004 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 25144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1258 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 19.4500 - 3.3900 1.00 2720 144 0.1493 0.1779 REMARK 3 2 3.3900 - 2.6900 1.00 2692 141 0.1665 0.1824 REMARK 3 3 2.6900 - 2.3500 1.00 2680 141 0.1763 0.2148 REMARK 3 4 2.3500 - 2.1400 1.00 2671 141 0.1700 0.2182 REMARK 3 5 2.1400 - 1.9800 1.00 2670 140 0.1739 0.2237 REMARK 3 6 1.9800 - 1.8700 1.00 2654 140 0.1822 0.2188 REMARK 3 7 1.8700 - 1.7700 1.00 2660 140 0.1940 0.2227 REMARK 3 8 1.7700 - 1.7000 1.00 2666 140 0.2014 0.2338 REMARK 3 9 1.7000 - 1.6300 0.93 2473 131 0.2118 0.2465 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.528 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.95 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 : 0.017 1461 REMARK 3 ANGLE : 1.485 1969 REMARK 3 CHIRALITY : 0.100 198 REMARK 3 PLANARITY : 0.011 245 REMARK 3 DIHEDRAL : 6.403 1196 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 7AOJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1292111525. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-03 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 : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25144 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 19.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 33.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.34330 REMARK 200 R SYM FOR SHELL (I) : 0.33900 REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1,6 AMMONIUM SULFATE, 0.5 M GLYCINE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.75667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.51333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.63500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 54.39167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 10.87833 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: 1250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 1 REMARK 465 ALA A 2 REMARK 465 CYS A 3 REMARK 465 GLN A 4 REMARK 465 VAL A 5 REMARK 465 ASP A 6 REMARK 465 ASN A 7 REMARK 465 PRO A 8 REMARK 465 PRO A 9 REMARK 465 LYS A 10 REMARK 465 THR A 11 REMARK 465 TYR A 12 REMARK 465 PRO A 13 REMARK 465 ASN A 14 REMARK 465 ASP A 15 REMARK 465 LYS A 16 REMARK 465 THR A 17 REMARK 465 ALA A 18 REMARK 465 GLU A 19 REMARK 465 TYR A 20 REMARK 465 GLU A 21 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 O1 GOL A 202 O HOH A 301 2.16 REMARK 500 NZ LYS A 154 O HOH A 302 2.18 REMARK 500 SG CYS A 115 O3 GOL A 202 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 102 17.20 53.31 REMARK 500 ASN A 133 2.40 80.01 REMARK 500 ASP A 139 41.76 -89.39 REMARK 500 GLU A 148 23.81 -158.96 REMARK 500 PHE A 169 19.63 55.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 205 DBREF 7AOJ A 1 179 UNP Q8I224 Q8I224_PLAF7 1 179 SEQRES 1 A 179 MET ALA CYS GLN VAL ASP ASN PRO PRO LYS THR TYR PRO SEQRES 2 A 179 ASN ASP LYS THR ALA GLU TYR GLU LYS TYR ALA ASN TYR SEQRES 3 A 179 MET ASN TYR LEU TYR TYR TYR GLN ASN ASN GLU LEU LYS SEQRES 4 A 179 LYS ILE ASP SER SER TYR PHE LYS ASP LYS TYR LEU GLY SEQRES 5 A 179 LEU PHE PHE GLY ALA SER TRP CYS LYS TYR CYS VAL THR SEQRES 6 A 179 PHE ILE ASP SER LEU ASN ILE PHE LYS LYS ASN PHE PRO SEQRES 7 A 179 ASN VAL GLU ILE ILE TYR ILE PRO PHE ASP ARG THR TYR SEQRES 8 A 179 GLN GLU TYR GLN SER PHE LEU LYS ASN THR ASN PHE TYR SEQRES 9 A 179 ALA LEU PRO PHE ASP ASN TYR LEU TYR ILE CYS LYS LYS SEQRES 10 A 179 TYR GLN ILE LYS ASN LEU PRO SER PHE MET LEU ILE THR SEQRES 11 A 179 PRO ASN ASN ASN ILE LEU VAL LYS ASP ALA ALA GLN LEU SEQRES 12 A 179 ILE LYS THR ASP GLU TYR ILE ASN ASN LEU LYS SER LEU SEQRES 13 A 179 ILE LYS ASN TYR ILE ILE HIS PRO LYS THR PHE GLN PHE SEQRES 14 A 179 ASN ASN ARG PHE PHE ASP LEU PHE ARG ASN HET GOL A 201 6 HET GOL A 202 6 HET GOL A 203 6 HET GOL A 204 6 HET GOL A 205 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 5(C3 H8 O3) FORMUL 7 HOH *149(H2 O) HELIX 1 AA1 SER A 44 LYS A 47 5 4 HELIX 2 AA2 CYS A 60 PHE A 77 1 18 HELIX 3 AA3 THR A 90 ASN A 102 1 13 HELIX 4 AA4 TYR A 111 TYR A 118 1 8 HELIX 5 AA5 ASP A 139 LYS A 145 1 7 HELIX 6 AA6 TYR A 149 TYR A 160 1 12 HELIX 7 AA7 PHE A 167 ASN A 171 5 5 HELIX 8 AA8 ARG A 172 ARG A 178 1 7 SHEET 1 AA1 2 TYR A 29 GLN A 34 0 SHEET 2 AA1 2 GLU A 37 ASP A 42 -1 O LYS A 39 N TYR A 32 SHEET 1 AA2 5 TYR A 104 ALA A 105 0 SHEET 2 AA2 5 GLU A 81 PRO A 86 1 N TYR A 84 O TYR A 104 SHEET 3 AA2 5 LEU A 51 GLY A 56 1 N PHE A 54 O ILE A 85 SHEET 4 AA2 5 SER A 125 ILE A 129 -1 O ILE A 129 N LEU A 51 SHEET 5 AA2 5 ILE A 135 VAL A 137 -1 O VAL A 137 N LEU A 128 CISPEP 1 LEU A 123 PRO A 124 0 -7.04 SITE 1 AC1 9 PHE A 108 ASP A 109 GLN A 119 ILE A 120 SITE 2 AC1 9 LYS A 121 ASN A 122 SER A 125 GOL A 204 SITE 3 AC1 9 HOH A 386 SITE 1 AC2 3 CYS A 115 LYS A 121 HOH A 301 SITE 1 AC3 6 TYR A 32 ASN A 102 TYR A 104 HOH A 308 SITE 2 AC3 6 HOH A 313 HOH A 358 SITE 1 AC4 8 TYR A 91 PHE A 108 ASN A 122 PRO A 124 SITE 2 AC4 8 SER A 125 ALA A 141 GOL A 201 HOH A 385 SITE 1 AC5 4 TYR A 23 ALA A 24 ASN A 25 TYR A 26 CRYST1 74.000 74.000 65.270 90.00 90.00 120.00 P 61 6 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 0.013514 0.007802 0.000000 0.00000 SCALE2 0.000000 0.015604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015321 0.00000