HEADER TRANSCRIPTION 13-FEB-19 6JGF TITLE CRYSTAL STRUCTURE OF SE-MET CADR FROM P. PUTIDA WITH A 21 RESIDUE C- TITLE 2 TERMINAL TRUNCATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CADR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CD(II)/PB(II)-RESPONSIVE TRANSCRIPTIONAL REGULATOR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_COMMON: ARTHROBACTER SIDEROCAPSULATUS; SOURCE 4 ORGANISM_TAXID: 303; SOURCE 5 ATCC: 47054; SOURCE 6 GENE: CADR, BIW19_10095, BL240_26950; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CADR, MERR FAMILY, CADMIUM REGULATOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR X.C.LIU,J.H.GAN,H.CHEN REVDAT 3 23-OCT-19 6JGF 1 JRNL REVDAT 2 09-OCT-19 6JGF 1 JRNL REVDAT 1 25-SEP-19 6JGF 0 JRNL AUTH X.LIU,Q.HU,J.YANG,S.HUANG,T.WEI,W.CHEN,Y.HE,D.WANG,Z.LIU, JRNL AUTH 2 K.WANG,J.GAN,H.CHEN JRNL TITL SELECTIVE CADMIUM REGULATION MEDIATED BY A COOPERATIVE JRNL TITL 2 BINDING MECHANISM IN CADR. JRNL REF PROC.NATL.ACAD.SCI.USA V. 116 20398 2019 JRNL REFN ESSN 1091-6490 JRNL PMID 31548408 JRNL DOI 10.1073/PNAS.1908610116 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 6753 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 382 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 477 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE SET COUNT : 28 REMARK 3 BIN FREE R VALUE : 0.3470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 940 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 28 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.59000 REMARK 3 B22 (A**2) : -0.59000 REMARK 3 B33 (A**2) : 1.90000 REMARK 3 B12 (A**2) : -0.29000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.306 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.240 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.191 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.840 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 960 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 943 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1295 ; 1.277 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2156 ; 0.919 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 116 ; 5.329 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 52 ;31.471 ;23.654 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 177 ;16.901 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;24.157 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 151 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1076 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 215 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 467 ; 3.048 ; 4.697 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 466 ; 3.046 ; 4.684 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 579 ; 4.962 ; 6.983 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 580 ; 4.962 ; 6.997 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 493 ; 3.602 ; 5.218 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 486 ; 3.596 ; 5.160 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 708 ; 5.843 ; 7.618 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1073 ; 8.239 ;36.225 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1073 ; 8.233 ;36.269 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6JGF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1300011013. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7330 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 72.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.80 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.056M SODIUM PHOSPHATE MONOBASIC, REMARK 280 1.344M POTASSIUM PHOSPHATE DIBASIC, PH 8.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 32.21167 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 64.42333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 64.42333 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 32.21167 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: 3880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 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 ALA A 30 REMARK 465 ARG A 31 REMARK 465 SER A 32 REMARK 465 ASP A 33 REMARK 465 GLY A 34 REMARK 465 ASN A 35 REMARK 465 TYR A 36 REMARK 465 ARG A 37 REMARK 465 CYS A 77 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 201 DBREF 6JGF A 1 126 UNP Q93TP7 Q93TP7_PSEPU 1 126 SEQRES 1 A 126 MSE LYS ILE GLY GLU LEU ALA LYS ALA THR ASP CYS ALA SEQRES 2 A 126 VAL GLU THR ILE ARG TYR TYR GLU ARG GLU GLN LEU LEU SEQRES 3 A 126 PRO GLU PRO ALA ARG SER ASP GLY ASN TYR ARG LEU TYR SEQRES 4 A 126 THR GLN ALA HIS VAL GLU ARG LEU THR PHE ILE ARG ASN SEQRES 5 A 126 CYS ARG THR LEU ASP MSE THR LEU ASP GLU ILE ARG SER SEQRES 6 A 126 LEU LEU ARG LEU ARG ASP SER PRO ASP ASP SER CYS GLY SEQRES 7 A 126 SER VAL ASN ALA LEU ILE ASP GLU HIS ILE GLU HIS VAL SEQRES 8 A 126 GLN ALA ARG ILE ASP GLY LEU VAL ALA LEU GLN GLU GLN SEQRES 9 A 126 LEU VAL GLU LEU ARG ARG ARG CYS ASN ALA GLN GLY ALA SEQRES 10 A 126 GLU CYS ALA ILE LEU GLN GLN LEU GLU MODRES 6JGF MSE A 1 MET MODIFIED RESIDUE MODRES 6JGF MSE A 58 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 58 8 HET PO4 A 201 5 HETNAM MSE SELENOMETHIONINE HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *28(H2 O) HELIX 1 AA1 LYS A 2 ASP A 11 1 10 HELIX 2 AA2 ALA A 13 GLU A 23 1 11 HELIX 3 AA3 THR A 40 THR A 55 1 16 HELIX 4 AA4 THR A 59 SER A 72 1 14 HELIX 5 AA5 SER A 79 LEU A 125 1 47 LINK C MSE A 1 N LYS A 2 1555 1555 1.33 LINK C ASP A 57 N MSE A 58 1555 1555 1.33 LINK C MSE A 58 N THR A 59 1555 1555 1.34 SITE 1 AC1 2 HIS A 90 ARG A 94 CRYST1 47.735 47.735 96.635 90.00 90.00 120.00 P 31 2 1 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 0.020949 0.012095 0.000000 0.00000 SCALE2 0.000000 0.024190 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010348 0.00000 HETATM 1 N MSE A 1 35.839 -2.995 -1.623 1.00 66.64 N HETATM 2 CA MSE A 1 35.108 -2.030 -2.491 1.00 68.80 C HETATM 3 C MSE A 1 35.703 -0.648 -2.395 1.00 67.92 C HETATM 4 O MSE A 1 36.089 -0.189 -1.307 1.00 62.50 O HETATM 5 CB MSE A 1 33.656 -2.014 -2.036 1.00 75.10 C HETATM 6 CG MSE A 1 32.671 -1.704 -3.147 1.00 78.63 C HETATM 7 SE MSE A 1 30.890 -2.115 -2.418 1.00 86.20 SE HETATM 8 CE MSE A 1 30.178 -2.871 -4.095 1.00 84.82 C