HEADER METAL BINDING PROTEIN 15-FEB-24 8W1D TITLE CRYSTAL STRUCTURE OF DPS-LIKE PROTEIN PA4880 FROM PSEUDOMONAS TITLE 2 AERUGINOSA (DIMERIC FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DPS-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 GENE: PA4880; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS PA4880, DPS PROTEIN, METAL BINDING, DNA CLEAVAGE, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.LOVELL,K.P.BATTAILE,M.RIVERA REVDAT 2 19-JUN-24 8W1D 1 JRNL REVDAT 1 29-MAY-24 8W1D 0 JRNL AUTH N.RAJAPAKSHA,H.YAO,A.COOK,S.SEIBOLD,L.LIU,K.P.BATTAILE, JRNL AUTH 2 L.FONTENOT,F.DONNARUMMA,S.LOVELL,M.RIVERA JRNL TITL PSEUDOMONAS AERUGINOSA GENE PA4880 ENCODES A DPS-LIKE JRNL TITL 2 PROTEIN WITH A DPS FOLD, BACTERIOFERRITIN-TYPE FERROXIDASE JRNL TITL 3 CENTERS, AND ENDONUCLEASE ACTIVITY. JRNL REF FRONT MOL BIOSCI V. 11 90745 2024 JRNL REFN ESSN 2296-889X JRNL PMID 38841187 JRNL DOI 10.3389/FMOLB.2024.1390745 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18RC4_3812: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32096 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1559 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 28.7600 - 2.8900 1.00 2852 147 0.1553 0.1861 REMARK 3 2 2.8900 - 2.2900 1.00 2796 139 0.1511 0.1649 REMARK 3 3 2.2900 - 2.0000 1.00 2785 140 0.1256 0.1588 REMARK 3 4 2.0000 - 1.8200 1.00 2773 139 0.1278 0.1666 REMARK 3 5 1.8200 - 1.6900 1.00 2782 152 0.1267 0.1819 REMARK 3 6 1.6900 - 1.5900 1.00 2764 132 0.1195 0.1787 REMARK 3 7 1.5900 - 1.5100 1.00 2773 130 0.1172 0.1812 REMARK 3 8 1.5100 - 1.4500 1.00 2765 149 0.1331 0.1807 REMARK 3 9 1.4500 - 1.3900 1.00 2752 147 0.1658 0.1927 REMARK 3 10 1.3900 - 1.3400 1.00 2737 160 0.1882 0.2206 REMARK 3 11 1.3400 - 1.3000 1.00 2758 124 0.2176 0.2674 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 1193 REMARK 3 ANGLE : 0.922 1614 REMARK 3 CHIRALITY : 0.056 182 REMARK 3 PLANARITY : 0.006 216 REMARK 3 DIHEDRAL : 14.936 450 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 8W1D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281638. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9201 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32140 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 28.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 1.18000 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: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROPLEX D5: 8% (W/V) PEG 6,000, 100 MM REMARK 280 MES PH 6.0, 100 MM MGCL2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 28.96900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.96900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.29000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 115.87600 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 THR A 2 REMARK 465 THR A 3 REMARK 465 VAL A 4 REMARK 465 GLN A 5 REMARK 465 LEU A 6 REMARK 465 THR A 7 REMARK 465 ASP A 8 REMARK 465 VAL A 9 REMARK 465 GLN A 10 REMARK 465 THR A 11 REMARK 465 LEU A 12 REMARK 465 ARG A 13 REMARK 465 ASP A 14 REMARK 465 ARG A 15 REMARK 465 ALA A 16 REMARK 465 ARG A 17 REMARK 465 LYS A 18 REMARK 465 ASN A 19 REMARK 465 ILE A 20 REMARK 465 GLN A 21 REMARK 465 GLU A 22 REMARK 465 GLY A 23 REMARK 465 ALA A 24 REMARK 465 VAL A 25 REMARK 465 THR A 26 REMARK 465 GLU A 27 REMARK 465 GLY A 28 REMARK 465 TYR A 29 REMARK 465 SER A 30 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 103 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 107 CD OE1 OE2 REMARK 470 ASN A 146 CG OD1 ND2 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 O HOH A 301 O HOH A 305 2.11 REMARK 500 OE2 GLU A 162 O HOH A 301 2.17 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 ASP A 148 77.45 -151.78 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 FE2 A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 47 OE1 REMARK 620 2 GLU A 47 OE2 59.2 REMARK 620 3 GLU A 80 OE1 95.0 153.9 REMARK 620 4 HIS A 83 ND1 110.2 102.0 90.0 REMARK 620 5 GLU A 162 OE2 127.8 82.8 114.3 111.8 REMARK 620 6 HOH A 301 O 79.8 89.5 81.4 167.5 64.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 202 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 80 OE2 REMARK 620 2 GLU A 130 OE1 130.4 REMARK 620 3 GLU A 130 OE2 89.2 57.2 REMARK 620 4 GLU A 162 OE1 120.8 87.9 144.8 REMARK 620 5 HIS A 165 ND1 106.6 110.0 92.6 95.4 REMARK 620 6 HOH A 305 O 69.6 70.9 83.2 90.2 174.3 REMARK 620 N 1 2 3 4 5 DBREF 8W1D A 1 177 UNP Q9HUT3 Q9HUT3_PSEAE 1 177 SEQRES 1 A 177 MET THR THR VAL GLN LEU THR ASP VAL GLN THR LEU ARG SEQRES 2 A 177 ASP ARG ALA ARG LYS ASN ILE GLN GLU GLY ALA VAL THR SEQRES 3 A 177 GLU GLY TYR SER ALA ASP ARG GLN THR VAL LEU ARG LEU SEQRES 4 A 177 LEU ASN GLU ALA LEU ALA THR GLU LEU VAL CYS PHE LEU SEQRES 5 A 177 ARG TYR LYS ARG HIS TYR PHE MET ALA THR GLY LEU LYS SEQRES 6 A 177 ALA SER ILE ALA ALA ALA GLU PHE LEU GLU HIS ALA ASN SEQRES 7 A 177 GLN GLU MET GLN HIS ALA ASP GLN LEU ALA GLU ARG ILE SEQRES 8 A 177 MET GLN LEU GLY GLY GLU PRO ASP PHE ASN PRO ARG GLY SEQRES 9 A 177 LEU GLU GLU ARG SER HIS ALA GLU TYR VAL GLU GLY LYS SEQRES 10 A 177 THR LEU LYS ASP MET VAL THR GLU ASN LEU ILE ALA GLU SEQRES 11 A 177 ARG ILE ALA ILE ASP SER TYR ARG GLU ILE ILE THR TYR SEQRES 12 A 177 LEU GLY ASN ASP ASP PRO THR THR ARG ARG ILE PHE GLU SEQRES 13 A 177 GLU ILE LEU ALA GLN GLU GLU GLU HIS ALA ASP ASP MET SEQRES 14 A 177 ALA ASP ILE LEU ASP ASP LEU ALA HET FE2 A 201 1 HET FE2 A 202 1 HETNAM FE2 FE (II) ION FORMUL 2 FE2 2(FE 2+) FORMUL 4 HOH *147(H2 O) HELIX 1 AA1 ASP A 32 LEU A 64 1 33 HELIX 2 AA2 ALA A 66 LEU A 94 1 29 HELIX 3 AA3 GLY A 104 SER A 109 1 6 HELIX 4 AA4 THR A 118 GLY A 145 1 28 HELIX 5 AA5 ASP A 148 ALA A 177 1 30 LINK OE1 GLU A 47 FE FE2 A 201 1555 1555 1.92 LINK OE2 GLU A 47 FE FE2 A 201 1555 1555 2.39 LINK OE1 GLU A 80 FE FE2 A 201 1555 1555 2.10 LINK OE2 GLU A 80 FE FE2 A 202 1555 1555 1.92 LINK ND1 HIS A 83 FE FE2 A 201 1555 1555 2.01 LINK OE1 GLU A 130 FE FE2 A 202 1555 1555 2.12 LINK OE2 GLU A 130 FE FE2 A 202 1555 1555 2.37 LINK OE2 GLU A 162 FE FE2 A 201 1555 1555 1.89 LINK OE1 GLU A 162 FE FE2 A 202 1555 1555 2.01 LINK ND1 HIS A 165 FE FE2 A 202 1555 1555 2.06 LINK FE FE2 A 201 O HOH A 301 1555 1555 2.16 LINK FE FE2 A 202 O HOH A 305 1555 1555 2.20 CRYST1 57.938 44.580 51.468 90.00 96.97 90.00 C 1 2 1 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 0.017260 0.000000 0.002111 0.00000 SCALE2 0.000000 0.022432 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019574 0.00000