HEADER UNKNOWN FUNCTION 06-JUL-12 4FZO TITLE CRYSTAL STRUCTURE OF THE APO-FORM URANYL BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: URANYL BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS; SOURCE 3 ORGANISM_TAXID: 187420; SOURCE 4 STRAIN: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / DELTA H; SOURCE 5 GENE: MTH_1690; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG19 KEYWDS URANYL BINDING, URANYL, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.HE,L.ZHOU,L.ZHANG REVDAT 3 28-FEB-24 4FZO 1 SEQADV REVDAT 2 21-MAY-14 4FZO 1 JRNL REVDAT 1 11-DEC-13 4FZO 0 JRNL AUTH L.ZHOU,M.BOSSCHER,C.ZHANG,S.OZCUBUKCU,L.ZHANG,W.ZHANG, JRNL AUTH 2 C.J.LI,J.LIU,M.P.JENSEN,L.LAI,C.HE JRNL TITL A PROTEIN ENGINEERED TO BIND URANYL SELECTIVELY AND WITH JRNL TITL 2 FEMTOMOLAR AFFINITY. JRNL REF NAT CHEM V. 6 236 2014 JRNL REFN ISSN 1755-4330 JRNL PMID 24557139 JRNL DOI 10.1038/NCHEM.1856 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 38.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 33856 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1715 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 38.2097 - 2.9699 0.98 2861 150 0.1710 0.1810 REMARK 3 2 2.9699 - 2.3574 0.99 2747 162 0.1658 0.1667 REMARK 3 3 2.3574 - 2.0594 0.99 2750 133 0.1535 0.1821 REMARK 3 4 2.0594 - 1.8711 1.00 2686 165 0.1591 0.1971 REMARK 3 5 1.8711 - 1.7370 0.99 2714 130 0.1601 0.1681 REMARK 3 6 1.7370 - 1.6346 1.00 2700 149 0.1508 0.1640 REMARK 3 7 1.6346 - 1.5527 1.00 2698 138 0.1426 0.1604 REMARK 3 8 1.5527 - 1.4851 1.00 2699 137 0.1418 0.1412 REMARK 3 9 1.4851 - 1.4280 1.00 2673 155 0.1567 0.1611 REMARK 3 10 1.4280 - 1.3787 0.99 2677 137 0.1595 0.2074 REMARK 3 11 1.3787 - 1.3356 0.97 2629 131 0.1590 0.1853 REMARK 3 12 1.3356 - 1.3000 0.86 2307 128 0.1558 0.1911 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31780 REMARK 3 B22 (A**2) : -0.30140 REMARK 3 B33 (A**2) : -0.01650 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1387 REMARK 3 ANGLE : 1.094 1875 REMARK 3 CHIRALITY : 0.076 212 REMARK 3 PLANARITY : 0.004 245 REMARK 3 DIHEDRAL : 13.524 562 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 4FZO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073553. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34522 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 38.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 15.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 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: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, TACSIMATE 4.0, SODIUM REMARK 280 ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 22.12800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.72150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.51700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.72150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.12800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.51700 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: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER B -2 REMARK 465 ASN B -1 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 OE1 GLU B 17 O HOH B 197 2.10 REMARK 500 OD2 ASP A 13 O HOH A 176 2.12 REMARK 500 OD1 ASP A 13 O HOH A 160 2.14 REMARK 500 NZ LYS A 22 O HOH A 132 2.16 REMARK 500 OD1 ASP B 68 O HOH B 197 2.17 REMARK 500 O HOH B 169 O HOH B 170 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 161 O HOH B 143 2554 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FZP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE URANYL BINDING PROTEIN COMPLEXED WITH REMARK 900 URANYL DBREF 4FZO A 2 77 UNP O27725 O27725_METTH 2 77 DBREF 4FZO B 2 77 UNP O27725 O27725_METTH 2 77 SEQADV 4FZO SER A -2 UNP O27725 EXPRESSION TAG SEQADV 4FZO ASN A -1 UNP O27725 EXPRESSION TAG SEQADV 4FZO ALA A 0 UNP O27725 EXPRESSION TAG SEQADV 4FZO LEU A 1 UNP O27725 EXPRESSION TAG SEQADV 4FZO ASP A 13 UNP O27725 LEU 13 ENGINEERED MUTATION SEQADV 4FZO GLU A 17 UNP O27725 ASN 17 ENGINEERED MUTATION SEQADV 4FZO GLU A 64 UNP O27725 HIS 64 ENGINEERED MUTATION SEQADV 4FZO THR A 67 UNP O27725 LEU 67 ENGINEERED MUTATION SEQADV 4FZO GLU A 78 UNP O27725 EXPRESSION TAG SEQADV 4FZO GLY A 79 UNP O27725 EXPRESSION TAG SEQADV 4FZO SER B -2 UNP O27725 EXPRESSION TAG SEQADV 4FZO ASN B -1 UNP O27725 EXPRESSION TAG SEQADV 4FZO ALA B 0 UNP O27725 EXPRESSION TAG SEQADV 4FZO LEU B 1 UNP O27725 EXPRESSION TAG SEQADV 4FZO ASP B 13 UNP O27725 LEU 13 ENGINEERED MUTATION SEQADV 4FZO GLU B 17 UNP O27725 ASN 17 ENGINEERED MUTATION SEQADV 4FZO GLU B 64 UNP O27725 HIS 64 ENGINEERED MUTATION SEQADV 4FZO THR B 67 UNP O27725 LEU 67 ENGINEERED MUTATION SEQADV 4FZO GLU B 78 UNP O27725 EXPRESSION TAG SEQADV 4FZO GLY B 79 UNP O27725 EXPRESSION TAG SEQRES 1 A 82 SER ASN ALA LEU ASP CYS ARG GLU ARG ILE GLU LYS ASP SEQRES 2 A 82 LEU GLU ASP LEU GLU LYS GLU LEU MET GLU MET LYS SER SEQRES 3 A 82 ILE LYS LEU SER ASP ASP GLU GLU ALA VAL VAL GLU ARG SEQRES 4 A 82 ALA LEU ASN TYR ARG ASP ASP SER VAL TYR TYR LEU GLU SEQRES 5 A 82 LYS GLY ASP HIS ILE THR SER PHE GLY CYS ILE THR TYR SEQRES 6 A 82 ALA GLU GLY LEU THR ASP SER LEU ARG MET LEU HIS ARG SEQRES 7 A 82 ILE ILE GLU GLY SEQRES 1 B 82 SER ASN ALA LEU ASP CYS ARG GLU ARG ILE GLU LYS ASP SEQRES 2 B 82 LEU GLU ASP LEU GLU LYS GLU LEU MET GLU MET LYS SER SEQRES 3 B 82 ILE LYS LEU SER ASP ASP GLU GLU ALA VAL VAL GLU ARG SEQRES 4 B 82 ALA LEU ASN TYR ARG ASP ASP SER VAL TYR TYR LEU GLU SEQRES 5 B 82 LYS GLY ASP HIS ILE THR SER PHE GLY CYS ILE THR TYR SEQRES 6 B 82 ALA GLU GLY LEU THR ASP SER LEU ARG MET LEU HIS ARG SEQRES 7 B 82 ILE ILE GLU GLY FORMUL 3 HOH *183(H2 O) HELIX 1 1 ASN A -1 ASP A 2 5 4 HELIX 2 2 CYS A 3 SER A 23 1 21 HELIX 3 3 SER A 27 LYS A 50 1 24 HELIX 4 4 ASP A 52 LEU A 73 1 22 HELIX 5 5 CYS B 3 LYS B 22 1 20 HELIX 6 6 SER B 27 LYS B 50 1 24 HELIX 7 7 ASP B 52 LEU B 73 1 22 CRYST1 44.256 47.034 65.443 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 0.022596 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021261 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015280 0.00000