HEADER HYDROLASE 28-JUL-11 3ZW7 TITLE THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN TITLE 2 COMPLEX WITH THE ALPHA-MANNOSYLGLYCERATE AND METAPHOSPHATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MPGP; COMPND 5 EC: 3.1.3.70; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 262724; SOURCE 4 STRAIN: HB27; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PKK223-3 KEYWDS HYDROLASE, HALOALKANOID ACID DEHALOGENASE-LIKE PHOSPHATASE, HAD-LIKE KEYWDS 2 PHOSPHATASE, CRYSTALLOGRAPHIC SNAPSHOT EXPDTA X-RAY DIFFRACTION AUTHOR S.GONCALVES,A.M.ESTEVES,H.SANTOS,N.BORGES,P.M.MATIAS REVDAT 4 20-DEC-23 3ZW7 1 HETSYN REVDAT 3 29-JUL-20 3ZW7 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 09-NOV-11 3ZW7 1 JRNL REVDAT 1 19-OCT-11 3ZW7 0 JRNL AUTH S.GONCALVES,A.M.ESTEVES,H.SANTOS,N.BORGES,P.M.MATIAS JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF JRNL TITL 2 MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE FROM THERMUS JRNL TITL 3 THERMOPHILUS HB27: A NEW MEMBER OF THE HALOALKANOIC ACID JRNL TITL 4 DEHALOGENASE SUPERFAMILY. JRNL REF BIOCHEMISTRY V. 50 9551 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21961705 JRNL DOI 10.1021/BI201171H REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.GONCALVES,A.M.ESTEVES,N.BORGES,H.SANTOS,P.M.MATIAS REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF REMARK 1 TITL 2 MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE FROM THERMUS REMARK 1 TITL 3 THERMOPHILUS HB27. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 67 390 2011 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 21393850 REMARK 1 DOI 10.1107/S1744309111002843 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.670 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 39897 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2020 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 24.9604 - 4.0847 0.90 3535 189 0.1522 0.1835 REMARK 3 2 4.0847 - 3.2444 0.99 3817 211 0.1564 0.2008 REMARK 3 3 3.2444 - 2.8349 1.00 3872 191 0.1675 0.2033 REMARK 3 4 2.8349 - 2.5760 1.00 3845 205 0.1632 0.2113 REMARK 3 5 2.5760 - 2.3915 1.00 3836 212 0.1553 0.1742 REMARK 3 6 2.3915 - 2.2506 1.00 3834 193 0.1622 0.2211 REMARK 3 7 2.2506 - 2.1380 1.00 3841 197 0.1603 0.2247 REMARK 3 8 2.1380 - 2.0450 1.00 3827 229 0.1737 0.2398 REMARK 3 9 2.0450 - 1.9663 1.00 3822 201 0.1982 0.2309 REMARK 3 10 1.9663 - 1.8984 0.96 3648 192 0.2326 0.2758 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 : 0.83 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 56.07 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.33720 REMARK 3 B22 (A**2) : 4.12400 REMARK 3 B33 (A**2) : -2.78680 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.58310 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 4042 REMARK 3 ANGLE : 1.009 5498 REMARK 3 CHIRALITY : 0.066 598 REMARK 3 PLANARITY : 0.005 730 REMARK 3 DIHEDRAL : 13.209 1545 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:32) REMARK 3 ORIGIN FOR THE GROUP (A): 37.4642 49.8878 -17.1170 REMARK 3 T TENSOR REMARK 3 T11: 0.7544 T22: 0.3710 REMARK 3 T33: 0.7090 T12: 0.0825 REMARK 3 T13: -0.0117 T23: -0.0228 REMARK 3 L TENSOR REMARK 3 L11: 0.5197 L22: 0.4118 REMARK 3 L33: 0.8358 L12: 0.0866 REMARK 3 L13: 0.4468 L23: 0.3251 REMARK 3 S TENSOR REMARK 3 S11: -0.0914 S12: -0.0917 S13: -1.0900 REMARK 3 S21: -0.2852 S22: 0.2733 S23: 0.0096 REMARK 3 S31: 1.6287 S32: 0.0712 S33: 0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 33:145) REMARK 3 ORIGIN FOR THE GROUP (A): 34.3381 61.9493 1.0023 REMARK 3 T TENSOR REMARK 3 T11: 0.1216 T22: 0.2184 REMARK 3 T33: 0.2582 T12: 0.0189 REMARK 3 T13: -0.0099 T23: 0.0433 REMARK 3 L TENSOR REMARK 3 L11: 1.3609 L22: 1.2263 REMARK 3 L33: 2.5398 L12: 0.6057 REMARK 3 L13: -1.0713 L23: -0.6742 REMARK 3 S TENSOR REMARK 3 S11: -0.0071 S12: -0.1587 S13: -0.0290 REMARK 3 S21: 0.0181 S22: -0.0520 S23: -0.0737 REMARK 3 S31: 0.0617 S32: 0.1015 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 146:175) REMARK 3 ORIGIN FOR THE GROUP (A): 18.7566 64.1462 2.0444 REMARK 3 T TENSOR REMARK 3 T11: 0.2280 T22: 0.4239 REMARK 3 T33: 0.3665 T12: 0.0049 REMARK 3 T13: -0.0189 T23: 0.0560 REMARK 3 L TENSOR REMARK 3 L11: 0.8044 L22: 0.6473 REMARK 3 L33: 1.2936 L12: -0.3032 REMARK 3 L13: 0.6998 L23: -0.1632 REMARK 3 S TENSOR REMARK 3 S11: 0.2085 S12: 0.0334 S13: -0.4249 REMARK 3 S21: -0.2192 S22: -0.0593 S23: 0.2828 REMARK 3 S31: 0.3491 S32: -0.9205 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 176:252) REMARK 3 ORIGIN FOR THE GROUP (A): 29.8698 58.9012 -20.9916 REMARK 3 T TENSOR REMARK 3 T11: 0.3778 T22: 0.2811 REMARK 3 T33: 0.3809 T12: -0.0565 REMARK 3 T13: -0.0991 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 2.5393 L22: 2.4293 REMARK 3 L33: 2.5405 L12: -1.1662 REMARK 3 L13: 0.8725 L23: -0.2946 REMARK 3 S TENSOR REMARK 3 S11: 0.1277 S12: 0.4707 S13: -0.5108 REMARK 3 S21: -0.4514 S22: 0.1759 S23: 0.4185 REMARK 3 S31: 0.6599 S32: -0.0932 S33: 0.0002 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 1:96) REMARK 3 ORIGIN FOR THE GROUP (A): 23.2210 49.6686 41.0798 REMARK 3 T TENSOR REMARK 3 T11: 0.4522 T22: 0.2787 REMARK 3 T33: 0.2234 T12: 0.0101 REMARK 3 T13: -0.0424 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 1.4411 L22: 0.5366 REMARK 3 L33: 3.6435 L12: 0.4872 REMARK 3 L13: -0.4622 L23: -0.3824 REMARK 3 S TENSOR REMARK 3 S11: 0.0823 S12: -0.1643 S13: 0.0983 REMARK 3 S21: 0.4512 S22: -0.1145 S23: -0.0558 REMARK 3 S31: -0.2969 S32: 0.2822 S33: 0.0001 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 97:124) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4073 52.2742 16.9002 REMARK 3 T TENSOR REMARK 3 T11: 0.2172 T22: 0.2594 REMARK 3 T33: 0.2759 T12: -0.0260 REMARK 3 T13: 0.0077 T23: -0.0212 REMARK 3 L TENSOR REMARK 3 L11: 1.1073 L22: 0.5173 REMARK 3 L33: 1.3508 L12: 0.4583 REMARK 3 L13: -0.0028 L23: -0.6848 REMARK 3 S TENSOR REMARK 3 S11: -0.0409 S12: 0.0773 S13: 0.0955 REMARK 3 S21: -0.1651 S22: -0.0413 S23: 0.0772 REMARK 3 S31: -0.1665 S32: 0.0184 S33: -0.0001 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN B AND RESID 125:175) REMARK 3 ORIGIN FOR THE GROUP (A): 18.3335 49.5093 23.4746 REMARK 3 T TENSOR REMARK 3 T11: 0.2218 T22: 0.2266 REMARK 3 T33: 0.2675 T12: 0.0080 REMARK 3 T13: 0.0140 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 1.6523 L22: 2.2333 REMARK 3 L33: 2.5914 L12: 0.0732 REMARK 3 L13: -0.7280 L23: -0.0728 REMARK 3 S TENSOR REMARK 3 S11: -0.0027 S12: 0.1362 S13: 0.2888 REMARK 3 S21: 0.2987 S22: 0.0685 S23: 0.4582 REMARK 3 S31: -0.2226 S32: -0.0617 S33: 0.0001 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN B AND RESID 176:252) REMARK 3 ORIGIN FOR THE GROUP (A): 8.9265 50.6016 45.6660 REMARK 3 T TENSOR REMARK 3 T11: 0.6132 T22: 0.3384 REMARK 3 T33: 0.2537 T12: 0.0413 REMARK 3 T13: 0.0878 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 1.9136 L22: 1.6431 REMARK 3 L33: 1.5420 L12: 0.9459 REMARK 3 L13: -0.2322 L23: 0.2346 REMARK 3 S TENSOR REMARK 3 S11: -0.0637 S12: -0.0067 S13: 0.2581 REMARK 3 S21: 0.3369 S22: 0.0668 S23: 0.3708 REMARK 3 S31: -0.2293 S32: -0.4428 S33: -0.0000 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 3ZW7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1290049212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95350 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : BENT CYLINDRICAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39808 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.920 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3ZTY REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SEE ACTAF REFERENCE IN REMARK 1 REMARK 280 ABOVE., PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 35.40200 REMARK 290 SMTRY3 2 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: 2220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.5 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 ARG A 254 REMARK 465 GLY A 255 REMARK 465 GLY A 256 REMARK 465 SER A 257 REMARK 465 GLY A 258 REMARK 465 PRO A 259 REMARK 465 ARG B 254 REMARK 465 GLY B 255 REMARK 465 GLY B 256 REMARK 465 SER B 257 REMARK 465 GLY B 258 REMARK 465 PRO B 259 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 ARG A 75 CG CD NE CZ REMARK 470 ASP A 223 CB CG OD1 OD2 REMARK 470 GLU A 226 CB CG CD OE1 OE2 REMARK 470 ARG A 253 CA C O CB CG CD NE REMARK 470 ARG A 253 CZ NH1 NH2 REMARK 470 GLU B 14 CG CD OE1 OE2 REMARK 470 ARG B 15 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 253 CA C O CB CG CD NE REMARK 470 ARG B 253 CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 7 -69.54 -97.75 REMARK 500 THR A 10 -74.12 -114.46 REMARK 500 GLU A 17 -149.22 -124.24 REMARK 500 LEU A 18 -100.14 -109.70 REMARK 500 TYR A 137 -48.93 -134.14 REMARK 500 LEU B 7 -71.21 -98.51 REMARK 500 THR B 10 -75.54 -110.96 REMARK 500 TYR B 137 -49.86 -132.37 REMARK 500 ASP B 202 -1.13 -151.49 REMARK 500 SER B 252 53.52 -107.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2028 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A2078 DISTANCE = 6.07 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 2-O-ALPHA-MANNOSYL-D-GLYCERATE (DMG): ASSIGNED PREVIOUSLY REMARK 600 WITH AS 2M8 IN 3ZU6 (HPUB) REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 260 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 6 OD2 REMARK 620 2 ASP A 8 O 78.5 REMARK 620 3 ASP A 202 OD1 61.6 71.7 REMARK 620 4 HOH A2009 O 74.1 142.2 72.5 REMARK 620 5 HOH A2222 O 135.3 103.3 76.4 79.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 260 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 6 OD2 REMARK 620 2 ASP B 8 O 103.1 REMARK 620 3 ASP B 202 OD1 90.0 73.0 REMARK 620 4 SER B 203 OG 78.3 144.6 71.6 REMARK 620 5 PO3 B 261 O3 99.9 80.9 153.6 134.2 REMARK 620 6 HOH B2007 O 162.9 69.7 73.1 98.5 94.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZWK RELATED DB: PDB REMARK 900 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, REMARK 900 IN COMPLEX WITH THE METAVANADATE REMARK 900 RELATED ID: 3ZUP RELATED DB: PDB REMARK 900 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, REMARK 900 IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE AND ORTHOPHOSPHATE REMARK 900 REACTION PRODUCTS. REMARK 900 RELATED ID: 3ZTY RELATED DB: PDB REMARK 900 THE 3-DIMENSIONAL STRUCTURE OF THE GADOLINIUM DERIVATIVE OF MPGP, REMARK 900 THE MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE FROM THERMUS REMARK 900 THERMOPHILUS HB27 REMARK 900 RELATED ID: 3ZTW RELATED DB: PDB REMARK 900 THE 3-DIMENSIONAL STRUCTURE OF APO-MPGP, THE MANNOSYL -3- REMARK 900 PHOSPHOGLYCERATE PHOSPHATASE FROM THERMUS THERMOPHILUS HB27 IN ITS REMARK 900 APO-FORM REMARK 900 RELATED ID: 3ZU6 RELATED DB: PDB REMARK 900 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, REMARK 900 IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE AND ORTHOPHOSPHATE REMARK 900 REACTION PRODUCTS. REMARK 900 RELATED ID: 3ZWD RELATED DB: PDB REMARK 900 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, REMARK 900 IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE. DBREF 3ZW7 A 1 259 UNP Q72K29 Q72K29_THET2 1 259 DBREF 3ZW7 B 1 259 UNP Q72K29 Q72K29_THET2 1 259 SEQRES 1 A 259 MET ILE VAL PHE THR ASP LEU ASP GLY THR LEU LEU ASP SEQRES 2 A 259 GLU ARG GLY GLU LEU GLY PRO ALA ARG GLU ALA LEU GLU SEQRES 3 A 259 ARG LEU ARG ALA LEU GLY VAL PRO VAL VAL PRO VAL THR SEQRES 4 A 259 ALA LYS THR ARG LYS GLU VAL GLU ALA LEU GLY LEU GLU SEQRES 5 A 259 PRO PRO PHE ILE VAL GLU ASN GLY GLY GLY LEU TYR LEU SEQRES 6 A 259 PRO ARG ASP TRP PRO VAL ARG ALA GLY ARG PRO LYS GLY SEQRES 7 A 259 GLY TYR ARG VAL VAL SER LEU ALA TRP PRO TYR ARG LYS SEQRES 8 A 259 VAL ARG ALA ARG LEU ARG GLU ALA GLU ALA LEU ALA GLY SEQRES 9 A 259 ARG PRO ILE LEU GLY TYR GLY ASP LEU THR ALA GLU ALA SEQRES 10 A 259 VAL ALA ARG LEU THR GLY LEU SER ARG GLU ALA ALA ARG SEQRES 11 A 259 ARG ALA LYS ALA ARG GLU TYR ASP GLU THR LEU VAL LEU SEQRES 12 A 259 CYS PRO GLU GLU VAL GLU ALA VAL LEU GLU ALA LEU GLU SEQRES 13 A 259 ALA VAL GLY LEU GLU TRP THR HIS GLY GLY ARG PHE TYR SEQRES 14 A 259 HIS ALA ALA LYS GLY ALA ASP LYS GLY ARG ALA VAL ALA SEQRES 15 A 259 ARG LEU ARG ALA LEU TRP PRO ASP PRO GLU GLU ALA ARG SEQRES 16 A 259 PHE ALA VAL GLY LEU GLY ASP SER LEU ASN ASP LEU PRO SEQRES 17 A 259 LEU PHE ARG ALA VAL ASP LEU ALA VAL TYR VAL GLY ARG SEQRES 18 A 259 GLY ASP PRO PRO GLU GLY VAL LEU ALA THR PRO ALA PRO SEQRES 19 A 259 GLY PRO GLU GLY PHE ARG TYR ALA VAL GLU ARG TYR LEU SEQRES 20 A 259 LEU PRO ARG LEU SER ARG ARG GLY GLY SER GLY PRO SEQRES 1 B 259 MET ILE VAL PHE THR ASP LEU ASP GLY THR LEU LEU ASP SEQRES 2 B 259 GLU ARG GLY GLU LEU GLY PRO ALA ARG GLU ALA LEU GLU SEQRES 3 B 259 ARG LEU ARG ALA LEU GLY VAL PRO VAL VAL PRO VAL THR SEQRES 4 B 259 ALA LYS THR ARG LYS GLU VAL GLU ALA LEU GLY LEU GLU SEQRES 5 B 259 PRO PRO PHE ILE VAL GLU ASN GLY GLY GLY LEU TYR LEU SEQRES 6 B 259 PRO ARG ASP TRP PRO VAL ARG ALA GLY ARG PRO LYS GLY SEQRES 7 B 259 GLY TYR ARG VAL VAL SER LEU ALA TRP PRO TYR ARG LYS SEQRES 8 B 259 VAL ARG ALA ARG LEU ARG GLU ALA GLU ALA LEU ALA GLY SEQRES 9 B 259 ARG PRO ILE LEU GLY TYR GLY ASP LEU THR ALA GLU ALA SEQRES 10 B 259 VAL ALA ARG LEU THR GLY LEU SER ARG GLU ALA ALA ARG SEQRES 11 B 259 ARG ALA LYS ALA ARG GLU TYR ASP GLU THR LEU VAL LEU SEQRES 12 B 259 CYS PRO GLU GLU VAL GLU ALA VAL LEU GLU ALA LEU GLU SEQRES 13 B 259 ALA VAL GLY LEU GLU TRP THR HIS GLY GLY ARG PHE TYR SEQRES 14 B 259 HIS ALA ALA LYS GLY ALA ASP LYS GLY ARG ALA VAL ALA SEQRES 15 B 259 ARG LEU ARG ALA LEU TRP PRO ASP PRO GLU GLU ALA ARG SEQRES 16 B 259 PHE ALA VAL GLY LEU GLY ASP SER LEU ASN ASP LEU PRO SEQRES 17 B 259 LEU PHE ARG ALA VAL ASP LEU ALA VAL TYR VAL GLY ARG SEQRES 18 B 259 GLY ASP PRO PRO GLU GLY VAL LEU ALA THR PRO ALA PRO SEQRES 19 B 259 GLY PRO GLU GLY PHE ARG TYR ALA VAL GLU ARG TYR LEU SEQRES 20 B 259 LEU PRO ARG LEU SER ARG ARG GLY GLY SER GLY PRO HET MG A 260 1 HET PO4 A1253 5 HET CL A1254 1 HET MG B 260 1 HET PO3 B 261 4 HET 2M8 B 262 18 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION HETNAM PO3 PHOSPHITE ION HETNAM 2M8 (2R)-3-HYDROXY-2-(ALPHA-D-MANNOPYRANOSYLOXY)PROPANOIC HETNAM 2 2M8 ACID HETSYN 2M8 2-O-ALPHA-MANNOSYL-D-GLYCERATE; (2R)-3-HYDROXY-2- HETSYN 2 2M8 (ALPHA-D-MANNOSYLOXY)PROPANOIC ACID; (2R)-3-HYDROXY-2- HETSYN 3 2M8 (D-MANNOSYLOXY)PROPANOIC ACID; (2R)-3-HYDROXY-2- HETSYN 4 2M8 (MANNOSYLOXY)PROPANOIC ACID FORMUL 3 MG 2(MG 2+) FORMUL 4 PO4 O4 P 3- FORMUL 5 CL CL 1- FORMUL 7 PO3 O3 P 3- FORMUL 8 2M8 C9 H16 O9 FORMUL 9 HOH *402(H2 O) HELIX 1 1 GLY A 19 LEU A 31 1 13 HELIX 2 2 THR A 42 LEU A 49 1 8 HELIX 3 3 GLU A 58 GLY A 60 5 3 HELIX 4 4 PRO A 88 GLY A 104 1 17 HELIX 5 5 TYR A 110 ASP A 112 5 3 HELIX 6 6 THR A 114 GLY A 123 1 10 HELIX 7 7 SER A 125 ALA A 134 1 10 HELIX 8 8 CYS A 144 GLU A 146 5 3 HELIX 9 9 GLU A 147 VAL A 158 1 12 HELIX 10 10 ASP A 176 LEU A 187 1 12 HELIX 11 11 ASP A 190 ARG A 195 1 6 HELIX 12 12 SER A 203 ASN A 205 5 3 HELIX 13 13 ASP A 206 VAL A 213 1 8 HELIX 14 14 PRO A 234 TYR A 246 1 13 HELIX 15 15 LEU A 247 SER A 252 1 6 HELIX 16 16 LEU B 7 LEU B 12 1 6 HELIX 17 17 ALA B 21 LEU B 31 1 11 HELIX 18 18 THR B 42 LEU B 49 1 8 HELIX 19 19 GLU B 58 GLY B 60 5 3 HELIX 20 20 PRO B 88 GLY B 104 1 17 HELIX 21 21 THR B 114 GLY B 123 1 10 HELIX 22 22 SER B 125 LYS B 133 1 9 HELIX 23 23 CYS B 144 GLU B 146 5 3 HELIX 24 24 GLU B 147 VAL B 158 1 12 HELIX 25 25 ASP B 176 LEU B 187 1 12 HELIX 26 26 ASP B 190 ARG B 195 1 6 HELIX 27 27 SER B 203 ASN B 205 5 3 HELIX 28 28 ASP B 206 VAL B 213 1 8 HELIX 29 29 PRO B 234 TYR B 246 1 13 HELIX 30 30 LEU B 247 LEU B 251 5 5 SHEET 1 AA 5 VAL A 35 PRO A 37 0 SHEET 2 AA 5 ILE A 2 THR A 5 1 O VAL A 3 N VAL A 36 SHEET 3 AA 5 ALA A 197 GLY A 201 1 O VAL A 198 N PHE A 4 SHEET 4 AA 5 LEU A 215 TYR A 218 1 O LEU A 215 N GLY A 199 SHEET 5 AA 5 LEU A 229 ALA A 230 1 O LEU A 229 N TYR A 218 SHEET 1 AB 4 PHE A 55 VAL A 57 0 SHEET 2 AB 4 GLY A 62 PRO A 66 -1 O GLY A 62 N VAL A 57 SHEET 3 AB 4 TYR A 80 SER A 84 -1 O ARG A 81 N LEU A 65 SHEET 4 AB 4 ARG A 75 LYS A 77 -1 O ARG A 75 N VAL A 82 SHEET 1 AC 3 GLU A 139 LEU A 141 0 SHEET 2 AC 3 TYR A 169 ALA A 172 -1 O TYR A 169 N LEU A 141 SHEET 3 AC 3 GLU A 161 HIS A 164 -1 O GLU A 161 N ALA A 172 SHEET 1 BA 5 VAL B 35 PRO B 37 0 SHEET 2 BA 5 ILE B 2 THR B 5 1 O VAL B 3 N VAL B 36 SHEET 3 BA 5 ALA B 197 GLY B 201 1 O VAL B 198 N PHE B 4 SHEET 4 BA 5 LEU B 215 TYR B 218 1 O LEU B 215 N GLY B 199 SHEET 5 BA 5 LEU B 229 ALA B 230 1 O LEU B 229 N TYR B 218 SHEET 1 BB 4 PHE B 55 VAL B 57 0 SHEET 2 BB 4 GLY B 62 PRO B 66 -1 O GLY B 62 N VAL B 57 SHEET 3 BB 4 TYR B 80 SER B 84 -1 O ARG B 81 N LEU B 65 SHEET 4 BB 4 ARG B 75 PRO B 76 -1 O ARG B 75 N VAL B 82 SHEET 1 BC 4 LEU B 108 GLY B 109 0 SHEET 2 BC 4 GLU B 139 VAL B 142 -1 O VAL B 142 N LEU B 108 SHEET 3 BC 4 TYR B 169 ALA B 172 -1 O TYR B 169 N LEU B 141 SHEET 4 BC 4 GLU B 161 HIS B 164 -1 O GLU B 161 N ALA B 172 SSBOND 1 CYS A 144 CYS B 144 1555 1555 2.04 LINK OD2 ASP A 6 MG MG A 260 1555 1555 2.44 LINK O ASP A 8 MG MG A 260 1555 1555 2.62 LINK OD1 ASP A 202 MG MG A 260 1555 1555 2.76 LINK MG MG A 260 O HOH A2009 1555 1555 2.73 LINK MG MG A 260 O HOH A2222 1555 1555 2.83 LINK OD2 ASP B 6 MG MG B 260 1555 1555 2.62 LINK O ASP B 8 MG MG B 260 1555 1555 2.70 LINK OD1 ASP B 202 MG MG B 260 1555 1555 2.87 LINK OG SER B 203 MG MG B 260 1555 1555 2.74 LINK MG MG B 260 O3 PO3 B 261 1555 1555 2.23 LINK MG MG B 260 O HOH B2007 1555 1555 2.86 CISPEP 1 PRO A 53 PRO A 54 0 4.30 CISPEP 2 PRO B 53 PRO B 54 0 4.17 CRYST1 39.794 70.804 92.770 90.00 95.54 90.00 P 1 21 1 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 0.025129 0.000000 0.002437 0.00000 SCALE2 0.000000 0.014123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010830 0.00000 MTRIX1 1 0.811790 0.010770 0.583850 -3.90817 1 MTRIX2 1 -0.002230 -0.999770 0.021540 110.13918 1 MTRIX3 1 0.583950 -0.018790 -0.811570 12.61545 1