HEADER METAL BINDING PROTEIN 09-DEC-25 9ZLO TITLE CRYSTAL STRUCTURE OF PROTEUS MIRABILIS UREE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UREASE ACCESSORY PROTEIN UREE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PROTEUS MIRABILIS; SOURCE 3 ORGANISM_TAXID: 584; SOURCE 4 GENE: UREE, PMI3686; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: PLYSS KEYWDS NICKEL, METALLOCHAPERONE, UREASE ACCESSORY PROTEIN, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.PAN,S.L.MUELLER,E.J.FURLONG REVDAT 1 25-MAR-26 9ZLO 0 JRNL AUTH J.PAN,S.L.MUELLER,N.TASNEEM,Y.WU,E.J.FURLONG JRNL TITL MOLECULAR STRUCTURE AND NICKEL-BINDING CAPACITY OF PROTEUS JRNL TITL 2 MIRABILIS UREE. JRNL REF ACTA CRYSTALLOGR D STRUCT 2026 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 41834538 JRNL DOI 10.1107/S2059798326001907 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25832 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1314 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 45.9800 - 4.1600 1.00 2912 154 0.1740 0.1880 REMARK 3 2 4.1600 - 3.3000 1.00 2762 153 0.1742 0.2081 REMARK 3 3 3.3000 - 2.8800 1.00 2735 141 0.2056 0.2504 REMARK 3 4 2.8800 - 2.6200 1.00 2718 131 0.1942 0.2205 REMARK 3 5 2.6200 - 2.4300 1.00 2697 142 0.1948 0.2218 REMARK 3 6 2.4300 - 2.2900 1.00 2685 155 0.1884 0.2733 REMARK 3 7 2.2900 - 2.1700 1.00 2680 145 0.1892 0.2233 REMARK 3 8 2.1700 - 2.0800 1.00 2672 152 0.2007 0.2434 REMARK 3 9 2.0800 - 2.0000 1.00 2657 141 0.2098 0.2539 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) : 0.207 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.673 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.65 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 2280 REMARK 3 ANGLE : 1.025 3081 REMARK 3 CHIRALITY : 0.064 358 REMARK 3 PLANARITY : 0.011 394 REMARK 3 DIHEDRAL : 17.020 860 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 9ZLO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1000302988. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-25 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95365 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 : AIMLESS 0.8.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25897 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.60 REMARK 200 R MERGE FOR SHELL (I) : 0.81300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 5, 15% PEG REMARK 280 6000, 5 % GLYCEROL WITH THE ADDITION OF MICROSEEDS. MICROSEEDS REMARK 280 WERE MADE FROM NEEDLE-LIKE CRYSTALS OBTAINED IN 0.16-0.22 M REMARK 280 AMMONIUM CITRATE DIBASIC; 16-22 % PEG 3350., VAPOR DIFFUSION, REMARK 280 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 19.19300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.48500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.99200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.48500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.19300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.99200 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: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 19.19300 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -44.99200 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 GLY A 148 REMARK 465 SER A 149 REMARK 465 SER A 150 REMARK 465 GLY A 151 REMARK 465 GLY A 152 REMARK 465 HIS A 153 REMARK 465 HIS A 154 REMARK 465 HIS A 155 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 465 ASP A 158 REMARK 465 HIS A 159 REMARK 465 HIS A 160 REMARK 465 HIS A 161 REMARK 465 THR B 19 REMARK 465 GLU B 20 REMARK 465 LYS B 21 REMARK 465 ALA B 145 REMARK 465 TYR B 146 REMARK 465 GLY B 147 REMARK 465 GLY B 148 REMARK 465 SER B 149 REMARK 465 SER B 150 REMARK 465 GLY B 151 REMARK 465 GLY B 152 REMARK 465 HIS B 153 REMARK 465 HIS B 154 REMARK 465 HIS B 155 REMARK 465 HIS B 156 REMARK 465 HIS B 157 REMARK 465 ASP B 158 REMARK 465 HIS B 159 REMARK 465 HIS B 160 REMARK 465 HIS B 161 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 287 DISTANCE = 5.89 ANGSTROMS DBREF 9ZLO A 1 161 UNP P17090 UREE_PROMH 1 161 DBREF 9ZLO B 1 161 UNP P17090 UREE_PROMH 1 161 SEQRES 1 A 161 MET LYS LYS PHE THR GLN ILE ILE ASP GLN GLN LYS ALA SEQRES 2 A 161 LEU GLU LEU THR SER THR GLU LYS PRO LYS LEU THR LEU SEQRES 3 A 161 CYS LEU THR MET ASP GLU ARG THR LYS SER ARG LEU LYS SEQRES 4 A 161 VAL ALA LEU SER ASP GLY GLN GLU ALA GLY LEU PHE LEU SEQRES 5 A 161 PRO ARG GLY THR VAL LEU LYS GLU GLY ASP ILE LEU LEU SEQRES 6 A 161 SER GLU GLU GLY ASP VAL VAL THR ILE GLU ALA ALA LYS SEQRES 7 A 161 GLU GLN VAL SER THR VAL TYR SER ASP ASP PRO LEU LEU SEQRES 8 A 161 LEU ALA ARG VAL CYS TYR HIS LEU GLY ASN ARG HIS VAL SEQRES 9 A 161 PRO LEU GLN ILE GLU ALA GLY TRP CYS ARG TYR PHE HIS SEQRES 10 A 161 ASP HIS VAL LEU ASP ASP MET ALA ARG GLY LEU GLY ALA SEQRES 11 A 161 THR VAL VAL VAL GLY LEU GLU LYS TYR GLN PRO GLU PRO SEQRES 12 A 161 GLY ALA TYR GLY GLY SER SER GLY GLY HIS HIS HIS HIS SEQRES 13 A 161 HIS ASP HIS HIS HIS SEQRES 1 B 161 MET LYS LYS PHE THR GLN ILE ILE ASP GLN GLN LYS ALA SEQRES 2 B 161 LEU GLU LEU THR SER THR GLU LYS PRO LYS LEU THR LEU SEQRES 3 B 161 CYS LEU THR MET ASP GLU ARG THR LYS SER ARG LEU LYS SEQRES 4 B 161 VAL ALA LEU SER ASP GLY GLN GLU ALA GLY LEU PHE LEU SEQRES 5 B 161 PRO ARG GLY THR VAL LEU LYS GLU GLY ASP ILE LEU LEU SEQRES 6 B 161 SER GLU GLU GLY ASP VAL VAL THR ILE GLU ALA ALA LYS SEQRES 7 B 161 GLU GLN VAL SER THR VAL TYR SER ASP ASP PRO LEU LEU SEQRES 8 B 161 LEU ALA ARG VAL CYS TYR HIS LEU GLY ASN ARG HIS VAL SEQRES 9 B 161 PRO LEU GLN ILE GLU ALA GLY TRP CYS ARG TYR PHE HIS SEQRES 10 B 161 ASP HIS VAL LEU ASP ASP MET ALA ARG GLY LEU GLY ALA SEQRES 11 B 161 THR VAL VAL VAL GLY LEU GLU LYS TYR GLN PRO GLU PRO SEQRES 12 B 161 GLY ALA TYR GLY GLY SER SER GLY GLY HIS HIS HIS HIS SEQRES 13 B 161 HIS ASP HIS HIS HIS FORMUL 3 HOH *194(H2 O) HELIX 1 AA1 ASP A 9 THR A 17 1 9 HELIX 2 AA2 THR A 29 THR A 34 1 6 HELIX 3 AA3 ASP A 88 ARG A 102 1 15 HELIX 4 AA4 ASP A 118 LEU A 128 1 11 HELIX 5 AA5 ASP B 9 GLU B 15 1 7 HELIX 6 AA6 ASP B 31 LYS B 35 5 5 HELIX 7 AA7 ASP B 88 ASN B 101 1 14 HELIX 8 AA8 ASP B 118 LEU B 128 1 11 SHEET 1 AA1 6 LEU A 24 LEU A 28 0 SHEET 2 AA1 6 VAL A 71 ALA A 76 1 O GLU A 75 N LEU A 26 SHEET 3 AA1 6 ILE A 63 SER A 66 -1 N LEU A 64 O VAL A 72 SHEET 4 AA1 6 LYS A 2 ILE A 8 -1 N ILE A 8 O ILE A 63 SHEET 5 AA1 6 GLU A 47 PHE A 51 1 O PHE A 51 N PHE A 4 SHEET 6 AA1 6 ARG A 37 ALA A 41 -1 N LEU A 38 O LEU A 50 SHEET 1 AA2 4 GLN A 107 GLU A 109 0 SHEET 2 AA2 4 TRP A 112 PHE A 116 -1 O TRP A 112 N GLU A 109 SHEET 3 AA2 4 GLU A 79 TYR A 85 -1 N VAL A 84 O CYS A 113 SHEET 4 AA2 4 THR A 131 GLU A 137 -1 O THR A 131 N TYR A 85 SHEET 1 AA3 6 THR B 25 LEU B 28 0 SHEET 2 AA3 6 VAL B 71 ALA B 76 1 O GLU B 75 N LEU B 28 SHEET 3 AA3 6 ILE B 63 SER B 66 -1 N LEU B 64 O VAL B 72 SHEET 4 AA3 6 LYS B 2 ILE B 8 -1 N ILE B 8 O ILE B 63 SHEET 5 AA3 6 GLU B 47 PHE B 51 1 O GLY B 49 N PHE B 4 SHEET 6 AA3 6 ARG B 37 ALA B 41 -1 N LEU B 38 O LEU B 50 SHEET 1 AA4 4 GLN B 107 GLU B 109 0 SHEET 2 AA4 4 TRP B 112 PHE B 116 -1 O ARG B 114 N GLN B 107 SHEET 3 AA4 4 LYS B 78 TYR B 85 -1 N VAL B 84 O CYS B 113 SHEET 4 AA4 4 THR B 131 LYS B 138 -1 O GLY B 135 N VAL B 81 CRYST1 38.386 89.984 106.970 90.00 90.00 90.00 P 21 21 21 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 0.026051 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009348 0.00000 MASTER 261 0 0 8 20 0 0 6 2438 2 0 26 END