PDB Short entry for 4IYS HEADER METAL TRANSPORT 29-JAN-13 4IYS 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; COMPND 4 FRAGMENT: CBS DOMAIN, UNP RESIDUES 430-584; COMPND 5 SYNONYM: ANCIENT CONSERVED DOMAIN-CONTAINING PROTEIN 2, CYCLIN-M2; COMPND 6 ENGINEERED: 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 TRANSPORTER, 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 4IYS 1 SEQADV REVDAT 1 05-MAR-14 4IYS 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. 1.80 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.830 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 18265 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1719 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 27.6701 - 4.1168 0.92 2547 129 0.1837 0.2106 REMARK 3 2 4.1168 - 3.2693 0.95 2607 125 0.1693 0.2239 REMARK 3 3 3.2693 - 2.8565 0.96 2686 94 0.1914 0.2483 REMARK 3 4 2.8565 - 2.5956 0.97 2669 146 0.2028 0.2328 REMARK 3 5 2.5956 - 2.4096 0.98 2675 169 0.2283 0.2805 REMARK 3 6 2.4096 - 2.2676 0.98 2742 131 0.2330 0.2845 REMARK 3 7 2.2676 - 2.1541 0.98 2625 139 0.2441 0.2664 REMARK 3 8 2.1541 - 2.0604 0.98 2711 158 0.2684 0.3124 REMARK 3 9 2.0604 - 1.9811 0.98 2686 170 0.2850 0.3062 REMARK 3 10 1.9811 - 1.9127 0.98 2698 167 0.3305 0.3844 REMARK 3 11 1.9127 - 1.8530 0.98 2698 135 0.4031 0.4186 REMARK 3 12 1.8530 - 1.8000 0.98 2663 156 0.4282 0.4700 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 44.21 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13210 REMARK 3 B22 (A**2) : -6.08500 REMARK 3 B33 (A**2) : 6.21720 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 : 0.011 1284 REMARK 3 ANGLE : 1.297 1740 REMARK 3 CHIRALITY : 0.080 205 REMARK 3 PLANARITY : 0.005 225 REMARK 3 DIHEDRAL : 14.357 486 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -11.5967 0.9071 -20.2802 REMARK 3 T TENSOR REMARK 3 T11: 0.1385 T22: 0.1357 REMARK 3 T33: 0.2365 T12: -0.0045 REMARK 3 T13: -0.0061 T23: -0.0246 REMARK 3 L TENSOR REMARK 3 L11: 1.3941 L22: 2.4515 REMARK 3 L33: 5.1464 L12: -0.5847 REMARK 3 L13: 0.5704 L23: -1.0302 REMARK 3 S TENSOR REMARK 3 S11: -0.0042 S12: -0.0316 S13: -0.0242 REMARK 3 S21: -0.0312 S22: -0.0150 S23: 0.1770 REMARK 3 S31: -0.1163 S32: -0.0526 S33: 0.0407 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 4IYS 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_1000077379. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-11 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 : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9723 REMARK 200 MONOCHROMATOR : ID23-1 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 : 18265 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 54.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 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 <I/SIGMA(I)> 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 (%): 54.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60MM NAH2PO4, 1.34M K2HPO4, PH 4.6, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 27.87700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.22650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.87700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.22650 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: 3220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 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 GLY A 557 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 ASP A 558 CG OD1 OD2 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 NH1 ARG A 454 O HOH A 698 2.03 REMARK 500 OH TYR A 518 O HOH A 704 2.05 REMARK 500 O TYR A 518 O HOH A 721 2.06 REMARK 500 O HOH A 649 O HOH A 681 2.08 REMARK 500 OE1 GLU A 485 O HOH A 715 2.09 REMARK 500 ND2 ASN A 433 O HOH A 726 2.10 REMARK 500 O HOH A 684 O HOH A 733 2.18 REMARK 500 O HOH A 630 O HOH A 692 2.19 REMARK 500 O HOH A 680 O HOH A 686 2.19 REMARK 500 OH TYR A 478 O HOH A 725 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 647 O HOH A 725 2455 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 REMARK 900 RELATED ID: 4IY4 RELATED DB: PDB DBREF 4IYS A 430 584 UNP Q9H8M5 CNNM2_HUMAN 430 584 SEQADV 4IYS MET A 429 UNP Q9H8M5 EXPRESSION TAG SEQRES 1 A 156 MET 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 THR LEU GLU ASP SEQRES 12 A 156 VAL ILE GLU GLU ILE ILE LYS SER GLU ILE LEU ASP GLU FORMUL 2 HOH *135(H2 O) HELIX 1 1 MET A 429 LYS A 444 1 16 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 ASP A 504 CYS A 508 5 5 HELIX 7 7 PRO A 510 ASN A 519 1 10 HELIX 8 8 LYS A 530 LYS A 540 1 11 HELIX 9 9 LEU A 569 GLU A 580 1 12 SHEET 1 A 4 THR A 451 PRO A 452 0 SHEET 2 A 4 PHE A 560 THR A 568 -1 O ILE A 566 N THR A 451 SHEET 3 A 4 LEU A 545 ASN A 552 -1 N ALA A 546 O VAL A 567 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 PRO A 482 N ILE A 459 SHEET 3 B 3 ILE A 491 PHE A 496 -1 O LEU A 495 N ILE A 481 CRYST1 55.754 64.453 53.953 90.00 90.00 90.00 P 21 21 2 4 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 0.017936 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018535 0.00000