HEADER TRANSPORT PROTEIN 26-FEB-14 4P1G TITLE CRYSTAL STRUCTURE OF THE BATEMAN DOMAIN OF MURINE MAGNESIUM TITLE 2 TRANSPORTER CNNM2 BOUND TO AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: METAL TRANSPORTER CNNM2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 430-580; COMPND 5 SYNONYM: ANCIENT CONSERVED DOMAIN-CONTAINING PROTEIN 2, MACDP2, COMPND 6 CYCLIN-M2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CNNM2, ACDP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MAGNESIUM HOMEOSTASIS, TRANSPORT, HYPOMAGNESEMIA, RARE DISEASES, KEYWDS 2 ACDP, CYCLIN M, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.CORRAL-RODRIGUEZ,M.STUIVER,G.ABASCAL-PALACIOS,T.DIERCKS, AUTHOR 2 I.OYENARTE,J.ERENO-ORBEA,J.A.ENCINAR,V.SPIWOK,H.TERASHIMA,A.ACCARDI, AUTHOR 3 D.MULLER,L.A.MARTINEZ-CRUZ REVDAT 3 27-DEC-23 4P1G 1 REMARK REVDAT 2 22-NOV-17 4P1G 1 SOURCE JRNL REMARK REVDAT 1 04-MAR-15 4P1G 0 JRNL AUTH M.A.CORRAL-RODRIGUEZ,M.STUIVER,G.ABASCAL-PALACIOS,T.DIERCKS, JRNL AUTH 2 I.OYENARTE,J.ERENO-ORBEA,J.A.ENCINAR,V.SPIWOK,H.TERASHIMA, JRNL AUTH 3 A.ACCARDI,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. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 8072 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 901 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 28.1514 - 5.9419 1.00 1284 146 0.1853 0.2226 REMARK 3 2 5.9419 - 4.7235 1.00 1257 141 0.1787 0.2118 REMARK 3 3 4.7235 - 4.1285 1.00 1283 132 0.1601 0.1952 REMARK 3 4 4.1285 - 3.7520 1.00 1267 135 0.1928 0.2299 REMARK 3 5 3.7520 - 3.4836 1.00 1269 144 0.2456 0.2807 REMARK 3 6 3.4836 - 3.2785 1.00 1272 140 0.2499 0.3357 REMARK 3 7 3.2785 - 3.1145 1.00 1257 137 0.2634 0.2728 REMARK 3 8 3.1145 - 2.9791 1.00 1286 150 0.3105 0.3326 REMARK 3 9 2.9791 - 2.8645 1.00 1268 135 0.3392 0.4275 REMARK 3 10 2.8645 - 2.7658 1.00 1267 133 0.3292 0.3850 REMARK 3 11 2.7658 - 2.6794 1.00 1258 166 0.3317 0.4411 REMARK 3 12 2.6794 - 2.6030 0.96 1214 131 0.4315 0.4941 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 : 0.32 REMARK 3 B_SOL : 51.96 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 86.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.84680 REMARK 3 B22 (A**2) : -3.84680 REMARK 3 B33 (A**2) : 7.69360 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 1259 REMARK 3 ANGLE : 1.153 1707 REMARK 3 CHIRALITY : 0.073 199 REMARK 3 PLANARITY : 0.004 217 REMARK 3 DIHEDRAL : 15.209 472 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 4P1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000200501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-13 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8072 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 28.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 13.71 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 53.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA ACETATE PH 4.6, 3 M AMMONIUM REMARK 280 ACETATE, 10 MM AMP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-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 52.78950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 52.78950 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.10100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.78950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.55050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.78950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.65150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.78950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 76.65150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.78950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.55050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 52.78950 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 52.78950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.10100 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 52.78950 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 52.78950 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 51.10100 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 52.78950 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 76.65150 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 52.78950 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 25.55050 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 52.78950 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 25.55050 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 52.78950 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 76.65150 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 52.78950 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 52.78950 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 51.10100 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: 3810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 SER A 543 OG REMARK 470 GLU A 556 CG CD OE1 OE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP A 1000 DBREF 4P1G A 430 580 UNP Q3TWN3 CNNM2_MOUSE 430 580 SEQADV 4P1G MET A 429 UNP Q3TWN3 INITIATING METHIONINE SEQRES 1 A 152 MET GLU GLU LEU ASN ILE ILE GLN GLY ALA LEU GLU LEU SEQRES 2 A 152 ARG THR LYS THR VAL GLU ASP VAL MET THR PRO LEU ARG SEQRES 3 A 152 ASP CYS PHE MET ILE THR GLY GLU ALA ILE LEU ASP PHE SEQRES 4 A 152 ASN THR MET SER GLU ILE MET GLU SER GLY TYR THR ARG SEQRES 5 A 152 ILE PRO VAL PHE GLU GLY GLU ARG SER ASN ILE VAL ASP SEQRES 6 A 152 LEU LEU PHE VAL LYS ASP LEU ALA PHE VAL ASP PRO ASP SEQRES 7 A 152 ASP CYS THR PRO LEU LYS THR ILE THR LYS PHE TYR ASN SEQRES 8 A 152 HIS PRO LEU HIS PHE VAL PHE ASN ASP THR LYS LEU ASP SEQRES 9 A 152 ALA MET LEU GLU GLU PHE LYS LYS GLY LYS SER HIS LEU SEQRES 10 A 152 ALA ILE VAL GLN ARG VAL ASN ASN GLU GLY GLU GLY ASP SEQRES 11 A 152 PRO PHE TYR GLU VAL LEU GLY ILE VAL THR LEU GLU ASP SEQRES 12 A 152 VAL ILE GLU GLU ILE ILE LYS SER GLU HET AMP A1000 23 HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 AMP C10 H14 N5 O7 P HELIX 1 AA1 MET A 429 LEU A 441 1 13 HELIX 2 AA2 THR A 445 MET A 450 1 6 HELIX 3 AA3 ARG A 454 CYS A 456 5 3 HELIX 4 AA4 ASP A 466 SER A 476 1 11 HELIX 5 AA5 LYS A 498 ALA A 501 5 4 HELIX 6 AA6 ASP A 504 CYS A 508 5 5 HELIX 7 AA7 LEU A 511 ASN A 519 1 9 HELIX 8 AA8 LYS A 530 LYS A 540 1 11 HELIX 9 AA9 LEU A 569 LYS A 578 1 10 SHEET 1 AA1 4 THR A 451 PRO A 452 0 SHEET 2 AA1 4 PHE A 560 THR A 568 -1 O ILE A 566 N THR A 451 SHEET 3 AA1 4 LEU A 545 ASN A 552 -1 N ARG A 550 O GLU A 562 SHEET 4 AA1 4 PHE A 524 PHE A 526 1 N VAL A 525 O GLN A 549 SHEET 1 AA2 3 ILE A 459 THR A 460 0 SHEET 2 AA2 3 ARG A 480 PHE A 484 1 O PHE A 484 N ILE A 459 SHEET 3 AA2 3 ILE A 491 PHE A 496 -1 O LEU A 495 N ILE A 481 SHEET 1 AA3 2 ILE A 464 LEU A 465 0 SHEET 2 AA3 2 THR A 509 PRO A 510 -1 O THR A 509 N LEU A 465 CISPEP 1 GLY A 555 GLU A 556 0 -8.20 SITE 1 AC1 9 ASP A 455 CYS A 456 PHE A 457 TYR A 478 SITE 2 AC1 9 THR A 479 ARG A 480 PRO A 482 THR A 568 SITE 3 AC1 9 ASP A 571 CRYST1 105.579 105.579 102.202 90.00 90.00 90.00 I 41 2 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 0.009472 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009785 0.00000