HEADER METAL TRANSPORT 28-JAN-13 4IY4 TITLE STRUCTURAL AND LIGAND BINDING PROPERTIES OF THE BATEMAN DOMAIN OF TITLE 2 HUMAN MAGNESIUM TRANSPORTERS CNNM2 AND CNNM4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METAL TRANSPORTER CNNM2; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: CBS DOMAIN, UNP RESIDUES 429-584; COMPND 5 SYNONYM: ANCIENT CONSERVED DOMAIN-CONTAINING PROTEIN 2, CYCLIN-M2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CNNM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET101D/TOPO KEYWDS CBS DOMAIN, BATEMAN DOMAIN, MAGNESIUM TRANSPORT, MAGNESIUM SENSOR, KEYWDS 2 CYTOSOL, METAL TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.A.CORRAL-RODRIGUEZ,M.STUIVER,J.A.ENCINAR,V.SPIWOK,I.GOMEZ-GARCIA, AUTHOR 2 I.OYENARTE,J.ERENO-ORBEA,H.TERASHIMA,A.ACCARDI,T.DIERCKS,D.MULLER, AUTHOR 3 L.A.MARTINEZ-CRUZ REVDAT 2 20-MAR-24 4IY4 1 SEQADV REVDAT 1 12-MAR-14 4IY4 0 JRNL AUTH M.A.CORRAL-RODRIGUEZ,M.STUIVER,J.A.ENCINAR,V.SPIWOK, JRNL AUTH 2 I.GOMEZ-GARCIA,I.OYENARTE,J.ERENO-ORBEA,H.TERASHIMA, JRNL AUTH 3 A.ACCARDI,T.DIERCKS,D.MULLER,L.A.MARTINEZ-CRUZ JRNL TITL STRUCTURAL AND LIGAND BINDING PROPERTIES OF THE BATEMAN JRNL TITL 2 DOMAIN OF HUMAN MAGNESIUM TRANSPORTERS CNNM2 AND CNNM4 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12499 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 617 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 46.2236 - 4.6025 1.00 3122 149 0.2051 0.2430 REMARK 3 2 4.6025 - 3.6536 1.00 2953 161 0.2123 0.2887 REMARK 3 3 3.6536 - 3.1919 1.00 2909 151 0.2700 0.3350 REMARK 3 4 3.1919 - 2.9001 1.00 2898 156 0.3195 0.3523 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 : 0.86 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 23.09 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.04590 REMARK 3 B22 (A**2) : 3.04590 REMARK 3 B33 (A**2) : -6.09170 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 : 0.004 2473 REMARK 3 ANGLE : 0.722 3342 REMARK 3 CHIRALITY : 0.051 390 REMARK 3 PLANARITY : 0.003 431 REMARK 3 DIHEDRAL : 13.222 932 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 4IY4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077355. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-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 : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 REMARK 200 MONOCHROMATOR : ID14-1 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12501 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.218 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 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) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8M AMMONIUM CHLORIDE, 4MM MANGANESE REMARK 280 (II) CHLORIDE, 100MM SODIUM ACETATE , PH 4.6, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 49.94950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.67300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.67300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.92425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.67300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.67300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.97475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.67300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.67300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 74.92425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.67300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.67300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.97475 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.94950 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: 2740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 ILE A 581 REMARK 465 LEU A 582 REMARK 465 ASP A 583 REMARK 465 GLU A 584 REMARK 465 ILE C 581 REMARK 465 LEU C 582 REMARK 465 ASP C 583 REMARK 465 GLU C 584 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 GLU A 556 CG CD OE1 OE2 REMARK 470 GLU C 556 CG CD OE1 OE2 REMARK 470 GLU C 580 OE2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IY0 RELATED DB: PDB REMARK 900 RELATED ID: 4IY2 RELATED DB: PDB REMARK 900 RELATED ID: 4IY3 RELATED DB: PDB DBREF 4IY4 A 429 584 UNP Q9H8M5 CNNM2_HUMAN 429 584 DBREF 4IY4 C 429 584 UNP Q9H8M5 CNNM2_HUMAN 429 584 SEQADV 4IY4 ILE A 568 UNP Q9H8M5 THR 568 ENGINEERED MUTATION SEQADV 4IY4 ILE C 568 UNP Q9H8M5 THR 568 ENGINEERED MUTATION SEQRES 1 A 156 LYS GLU GLU LEU ASN ILE ILE GLN GLY ALA LEU GLU LEU SEQRES 2 A 156 ARG THR LYS THR VAL GLU ASP VAL MET THR PRO LEU ARG SEQRES 3 A 156 ASP CYS PHE MET ILE THR GLY GLU ALA ILE LEU ASP PHE SEQRES 4 A 156 ASN THR MET SER GLU ILE MET GLU SER GLY TYR THR ARG SEQRES 5 A 156 ILE PRO VAL PHE GLU GLY GLU ARG SER ASN ILE VAL ASP SEQRES 6 A 156 LEU LEU PHE VAL LYS ASP LEU ALA PHE VAL ASP PRO ASP SEQRES 7 A 156 ASP CYS THR PRO LEU LYS THR ILE THR LYS PHE TYR ASN SEQRES 8 A 156 HIS PRO LEU HIS PHE VAL PHE ASN ASP THR LYS LEU ASP SEQRES 9 A 156 ALA MET LEU GLU GLU PHE LYS LYS GLY LYS SER HIS LEU SEQRES 10 A 156 ALA ILE VAL GLN ARG VAL ASN ASN GLU GLY GLU GLY ASP SEQRES 11 A 156 PRO PHE TYR GLU VAL LEU GLY ILE VAL ILE LEU GLU ASP SEQRES 12 A 156 VAL ILE GLU GLU ILE ILE LYS SER GLU ILE LEU ASP GLU SEQRES 1 C 156 LYS GLU GLU LEU ASN ILE ILE GLN GLY ALA LEU GLU LEU SEQRES 2 C 156 ARG THR LYS THR VAL GLU ASP VAL MET THR PRO LEU ARG SEQRES 3 C 156 ASP CYS PHE MET ILE THR GLY GLU ALA ILE LEU ASP PHE SEQRES 4 C 156 ASN THR MET SER GLU ILE MET GLU SER GLY TYR THR ARG SEQRES 5 C 156 ILE PRO VAL PHE GLU GLY GLU ARG SER ASN ILE VAL ASP SEQRES 6 C 156 LEU LEU PHE VAL LYS ASP LEU ALA PHE VAL ASP PRO ASP SEQRES 7 C 156 ASP CYS THR PRO LEU LYS THR ILE THR LYS PHE TYR ASN SEQRES 8 C 156 HIS PRO LEU HIS PHE VAL PHE ASN ASP THR LYS LEU ASP SEQRES 9 C 156 ALA MET LEU GLU GLU PHE LYS LYS GLY LYS SER HIS LEU SEQRES 10 C 156 ALA ILE VAL GLN ARG VAL ASN ASN GLU GLY GLU GLY ASP SEQRES 11 C 156 PRO PHE TYR GLU VAL LEU GLY ILE VAL ILE LEU GLU ASP SEQRES 12 C 156 VAL ILE GLU GLU ILE ILE LYS SER GLU ILE LEU ASP GLU HELIX 1 1 LYS A 429 GLU A 440 1 12 HELIX 2 2 THR A 445 MET A 450 1 6 HELIX 3 3 ARG A 454 CYS A 456 5 3 HELIX 4 4 ASP A 466 GLY A 477 1 12 HELIX 5 5 LYS A 498 ALA A 501 5 4 HELIX 6 6 LEU A 511 ASN A 519 1 9 HELIX 7 7 LYS A 530 LYS A 540 1 11 HELIX 8 8 LEU A 569 LYS A 578 1 10 HELIX 9 9 GLU C 430 GLU C 440 1 11 HELIX 10 10 LEU C 441 THR C 443 5 3 HELIX 11 11 THR C 445 MET C 450 1 6 HELIX 12 12 ARG C 454 CYS C 456 5 3 HELIX 13 13 ASP C 466 SER C 476 1 11 HELIX 14 14 LYS C 498 ALA C 501 5 4 HELIX 15 15 LEU C 511 ASN C 519 1 9 HELIX 16 16 LYS C 530 LYS C 540 1 11 HELIX 17 17 LEU C 569 LYS C 578 1 10 SHEET 1 A 4 THR A 451 PRO A 452 0 SHEET 2 A 4 PHE A 560 ILE A 568 -1 O ILE A 566 N THR A 451 SHEET 3 A 4 LEU A 545 ASN A 552 -1 N VAL A 548 O LEU A 564 SHEET 4 A 4 PHE A 524 PHE A 526 1 N VAL A 525 O ILE A 547 SHEET 1 B 3 ILE A 459 THR A 460 0 SHEET 2 B 3 ARG A 480 PHE A 484 1 O PHE A 484 N ILE A 459 SHEET 3 B 3 ILE A 491 PHE A 496 -1 O LEU A 495 N ILE A 481 SHEET 1 C 2 ILE A 464 LEU A 465 0 SHEET 2 C 2 THR A 509 PRO A 510 -1 O THR A 509 N LEU A 465 SHEET 1 D 4 THR C 451 PRO C 452 0 SHEET 2 D 4 PHE C 560 ILE C 568 -1 O ILE C 566 N THR C 451 SHEET 3 D 4 LEU C 545 ASN C 552 -1 N ASN C 552 O PHE C 560 SHEET 4 D 4 PHE C 524 PHE C 526 1 N VAL C 525 O ILE C 547 SHEET 1 E 3 ILE C 459 THR C 460 0 SHEET 2 E 3 ARG C 480 PHE C 484 1 O PHE C 484 N ILE C 459 SHEET 3 E 3 ILE C 491 PHE C 496 -1 O LEU C 495 N ILE C 481 SHEET 1 F 2 ILE C 464 LEU C 465 0 SHEET 2 F 2 THR C 509 PRO C 510 -1 O THR C 509 N LEU C 465 CISPEP 1 GLY A 555 GLU A 556 0 7.93 CISPEP 2 GLY C 555 GLU C 556 0 0.71 CRYST1 103.346 103.346 99.899 90.00 90.00 90.00 P 43 21 2 16 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 0.009676 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009676 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010010 0.00000