10 20 30 40 50 60 70 80 3ZUP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 19-JUL-11 3ZUP
TITLE THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS TITLE 2 THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- TITLE 3 MANNOSYLGLYCERATE AND ORTHOPHOSPHATE REACTION PRODUCTS.
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
EXPDTA X-RAY DIFFRACTION
AUTHOR S.GONCALVES,A.M.ESTEVES,H.SANTOS,N.BORGES,P.M.MATIAS
REVDAT 2 09-NOV-11 3ZUP 1 JRNL REVDAT 1 19-OCT-11 3ZUP 0
JRNL AUTH S.GONCALVES,A.M.ESTEVES,H.SANTOS,N.BORGES,P.M.MATIAS JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF MANNOSYL-3- JRNL TITL 2 PHOSPHOGLYCERATE PHOSPHATASE FROM THERMUS THERMOPHILUS JRNL TITL 3 HB27: A NEW MEMBER OF THE HALOALKANOIC ACID DEHALOGENASE JRNL TITL 4 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 ISSN 1744-3091 REMARK 1 PMID 21393850 REMARK 1 DOI 10.1107/S1744309111002843
REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 1.804 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.161 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.99 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.80 REMARK 3 NUMBER OF REFLECTIONS : 46849 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1829 REMARK 3 R VALUE (WORKING SET) : 0.1804 REMARK 3 FREE R VALUE : 0.2297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 2342 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 42.1724 - 3.8859 0.96 4615 258 0.1664 0.2025 REMARK 3 2 3.8859 - 3.0847 0.99 4574 239 0.1770 0.2234 REMARK 3 3 3.0847 - 2.6948 1.00 4534 243 0.1901 0.2624 REMARK 3 4 2.6948 - 2.4484 0.99 4476 223 0.1841 0.2206 REMARK 3 5 2.4484 - 2.2730 0.99 4495 234 0.1794 0.2551 REMARK 3 6 2.2730 - 2.1390 1.00 4476 238 0.1788 0.2281 REMARK 3 7 2.1390 - 2.0318 1.00 4496 256 0.1814 0.2237 REMARK 3 8 2.0318 - 1.9434 1.00 4466 226 0.1910 0.2528 REMARK 3 9 1.9434 - 1.8686 0.99 4428 216 0.2150 0.2824 REMARK 3 10 1.8686 - 1.8041 0.88 3947 209 0.2301 0.2771 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.394 REMARK 3 B_SOL : 58.876 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.24 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.6926 REMARK 3 B22 (A**2) : -6.4708 REMARK 3 B33 (A**2) : 3.7782 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 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 4099 REMARK 3 ANGLE : 1.032 5582 REMARK 3 CHIRALITY : 0.065 612 REMARK 3 PLANARITY : 0.005 736 REMARK 3 DIHEDRAL : 13.003 1578 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 1:29) REMARK 3 ORIGIN FOR THE GROUP (A): -15.5164 -45.5029 26.9670 REMARK 3 T TENSOR REMARK 3 T11: 0.4563 T22: 0.2935 REMARK 3 T33: 0.2616 T12: -0.0449 REMARK 3 T13: -0.0894 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.8499 L22: 1.0755 REMARK 3 L33: 0.3351 L12: -0.4313 REMARK 3 L13: -0.1441 L23: -0.1601 REMARK 3 S TENSOR REMARK 3 S11: 0.0448 S12: 0.5575 S13: -0.1286 REMARK 3 S21: -0.9527 S22: 0.1869 S23: 0.4443 REMARK 3 S31: 0.6738 S32: -0.0278 S33: 0.0024 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 30:107) REMARK 3 ORIGIN FOR THE GROUP (A): -17.1095 -26.6734 34.2588 REMARK 3 T TENSOR REMARK 3 T11: 0.0965 T22: 0.1822 REMARK 3 T33: 0.1845 T12: 0.0076 REMARK 3 T13: -0.0010 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 1.8423 L22: 1.8358 REMARK 3 L33: 1.0016 L12: 0.5145 REMARK 3 L13: 0.3457 L23: 0.2592 REMARK 3 S TENSOR REMARK 3 S11: -0.0230 S12: 0.0771 S13: 0.0990 REMARK 3 S21: 0.0099 S22: 0.1237 S23: 0.3781 REMARK 3 S31: -0.0711 S32: -0.1433 S33: -0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 108:189) REMARK 3 ORIGIN FOR THE GROUP (A): -7.3556 -25.2314 28.3780 REMARK 3 T TENSOR REMARK 3 T11: 0.0953 T22: 0.1549 REMARK 3 T33: 0.1243 T12: -0.0005 REMARK 3 T13: -0.0077 T23: -0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.5255 L22: 2.5669 REMARK 3 L33: 1.2333 L12: 0.3409 REMARK 3 L13: -0.1133 L23: -0.9842 REMARK 3 S TENSOR REMARK 3 S11: -0.0141 S12: 0.0784 S13: 0.0394 REMARK 3 S21: -0.1776 S22: 0.0499 S23: 0.0009 REMARK 3 S31: 0.0529 S32: 0.0503 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 190:252) REMARK 3 ORIGIN FOR THE GROUP (A): -7.7554 -46.9475 35.9793 REMARK 3 T TENSOR REMARK 3 T11: 0.1974 T22: 0.2060 REMARK 3 T33: 0.1900 T12: 0.0323 REMARK 3 T13: -0.0086 T23: 0.0326 REMARK 3 L TENSOR REMARK 3 L11: 2.0877 L22: 3.3313 REMARK 3 L33: 1.5037 L12: -0.4501 REMARK 3 L13: 0.7461 L23: 0.5685 REMARK 3 S TENSOR REMARK 3 S11: 0.0379 S12: 0.0239 S13: -0.2058 REMARK 3 S21: 0.0016 S22: 0.0663 S23: -0.0007 REMARK 3 S31: 0.2095 S32: 0.2802 S33: -0.0003 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 1:29) REMARK 3 ORIGIN FOR THE GROUP (A): 2.8972 13.2906 6.6986 REMARK 3 T TENSOR REMARK 3 T11: 0.3212 T22: 0.3582 REMARK 3 T33: 0.2833 T12: 0.0323 REMARK 3 T13: 0.0452 T23: -0.0321 REMARK 3 L TENSOR REMARK 3 L11: 1.4717 L22: 0.9536 REMARK 3 L33: 0.3952 L12: -0.1462 REMARK 3 L13: 0.3296 L23: -0.0829 REMARK 3 S TENSOR REMARK 3 S11: 0.0379 S12: -0.5117 S13: 0.5584 REMARK 3 S21: 0.3710 S22: -0.1816 S23: -0.0029 REMARK 3 S31: -0.2053 S32: -0.1623 S33: -0.0002 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 30:143) REMARK 3 ORIGIN FOR THE GROUP (A): -5.9021 -4.7262 2.8290 REMARK 3 T TENSOR REMARK 3 T11: 0.3712 T22: 0.1954 REMARK 3 T33: 0.1949 T12: -0.0015 REMARK 3 T13: -0.1027 T23: 0.0267 REMARK 3 L TENSOR REMARK 3 L11: 1.7548 L22: 5.0748 REMARK 3 L33: 1.4751 L12: 1.4474 REMARK 3 L13: -0.9208 L23: -2.1178 REMARK 3 S TENSOR REMARK 3 S11: -0.0501 S12: 0.2293 S13: 0.0790 REMARK 3 S21: -0.9704 S22: 0.3122 S23: 0.7442 REMARK 3 S31: 0.4168 S32: -0.1920 S33: -0.0007 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN B AND RESID 144:177) REMARK 3 ORIGIN FOR THE GROUP (A): 6.6513 -14.0180 6.0968 REMARK 3 T TENSOR REMARK 3 T11: 0.4700 T22: 0.3077 REMARK 3 T33: 0.5396 T12: 0.1442 REMARK 3 T13: 0.2562 T23: 0.1490 REMARK 3 L TENSOR REMARK 3 L11: 1.5966 L22: 2.0487 REMARK 3 L33: 0.6724 L12: 1.0281 REMARK 3 L13: -0.6782 L23: -0.7428 REMARK 3 S TENSOR REMARK 3 S11: -0.3471 S12: -0.4641 S13: -0.7298 REMARK 3 S21: -0.9900 S22: -0.6568 S23: -1.3421 REMARK 3 S31: 0.6947 S32: 0.4643 S33: -0.0256 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN B AND RESID 178:252) REMARK 3 ORIGIN FOR THE GROUP (A): 10.7931 8.5111 -1.4207 REMARK 3 T TENSOR REMARK 3 T11: 0.3530 T22: 0.3252 REMARK 3 T33: 0.2888 T12: 0.0821 REMARK 3 T13: 0.0993 T23: 0.1378 REMARK 3 L TENSOR REMARK 3 L11: 2.6257 L22: 2.9962 REMARK 3 L33: 1.0945 L12: 0.7374 REMARK 3 L13: -0.4011 L23: -1.2006 REMARK 3 S TENSOR REMARK 3 S11: 0.0058 S12: 0.0840 S13: 0.0567 REMARK 3 S21: -0.8278 S22: -0.5354 S23: -0.8863 REMARK 3 S31: 0.3132 S32: 0.6932 S33: -0.0006 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 3ZUP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUL-11. REMARK 100 THE PDBE ID CODE IS EBI-49108.
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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47907 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.80 REMARK 200 RESOLUTION RANGE LOW (A) : 60.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.3 REMARK 200 R MERGE (I) : 0.04 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.29 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) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.5 REMARK 200 R MERGE FOR SHELL (I) : 0.32 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.67 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 (%): 45.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SEE REFERENCE IN REMARK 1
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.68400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.22850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.02450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.22850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.68400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.02450 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: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.1 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS B 77 CD REMARK 480 GLU B 226 CD
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 -78.08 -100.37 REMARK 500 THR A 10 -70.18 -122.01 REMARK 500 TYR A 137 -49.80 -137.02 REMARK 500 ASP A 202 -2.12 -144.73 REMARK 500 LEU B 7 -83.06 -99.04 REMARK 500 THR B 10 -76.31 -124.12 REMARK 500 ALA B 73 149.11 178.36 REMARK 500 TYR B 137 -47.12 -136.92 REMARK 500 ALA B 172 -169.91 -164.40 REMARK 500 REMARK 500 REMARK: NULL
REMARK 600 REMARK 600 HETEROGEN REMARK 600 2-O-ALPHA-MANNOSYL-D-GLYCERATE (MG9): MONOMER LIBRARY REMARK 600 REFERENCE ENTRY 2M8
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 A1254 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 6 OD2 REMARK 620 2 ASP A 8 O 86.7 REMARK 620 3 HOH A2004 O 117.0 92.8 REMARK 620 4 ASP A 202 OD1 81.1 100.8 158.2 REMARK 620 5 HOH A2006 O 89.5 175.3 86.5 81.3 REMARK 620 6 HOH A2007 O 161.0 88.1 81.5 82.0 96.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1254 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2006 O REMARK 620 2 ASP B 6 OD2 113.1 REMARK 620 3 HOH B2007 O 90.4 87.0 REMARK 620 4 ASP B 8 O 91.4 84.7 171.5 REMARK 620 5 ASP B 202 OD1 160.8 83.6 80.8 99.8 REMARK 620 6 HOH B2009 O 75.4 167.2 102.9 85.6 89.9 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2M8 A1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2M8 B1256
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZTY RELATED DB: PDB REMARK 900 THE 3-DIMENSIONAL STRUCTURE OF THE GADOLINIUM DERIVATIVE REMARK 900 OF MPGP, THE MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE REMARK 900 FROM THERMUS THERMOPHILUS HB27 REMARK 900 RELATED ID: 3ZTW RELATED DB: PDB REMARK 900 THE 3-DIMENSIONAL STRUCTURE OF APO-MPGP, THE MANNOSYL REMARK 900 -3-PHOSPHOGLYCERATE PHOSPHATASE FROM THERMUS THERMOPHILUS REMARK 900 HB27 IN ITS APO-FORM REMARK 900 RELATED ID: 3ZU6 RELATED DB: PDB REMARK 900 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS REMARK 900 THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- REMARK 900 MANNOSYLGLYCERATE AND ORTHOPHOSPHATE REACTION PRODUCTS.
DBREF 3ZUP A 1 259 UNP Q72K29 Q72K29_THET2 1 259 DBREF 3ZUP 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 A1254 1 HET PO4 A1255 5 HET 2M8 A1256 18 HET MG B1254 1 HET PO4 B1255 5 HET 2M8 B1256 18
HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM 2M8 2-O-ALPHA-MANNOSYL-D-GLYCERATE
FORMUL 3 MG 2(MG 2+) FORMUL 4 PO4 2(O4 P 3-) FORMUL 5 2M8 2(C9 H16 O9) FORMUL 6 HOH *391(H2 O)
HELIX 1 1 LEU A 18 PRO A 20 5 3 HELIX 2 2 ALA A 21 LEU A 31 1 11 HELIX 3 3 THR A 42 LEU A 49 1 8 HELIX 4 4 GLU A 58 GLY A 60 5 3 HELIX 5 5 PRO A 88 GLY A 104 1 17 HELIX 6 6 TYR A 110 ASP A 112 5 3 HELIX 7 7 THR A 114 GLY A 123 1 10 HELIX 8 8 SER A 125 ALA A 134 1 10 HELIX 9 9 CYS A 144 GLU A 146 5 3 HELIX 10 10 GLU A 147 VAL A 158 1 12 HELIX 11 11 ASP A 176 TRP A 188 1 13 HELIX 12 12 ASP A 190 ARG A 195 1 6 HELIX 13 13 SER A 203 ASN A 205 5 3 HELIX 14 14 ASP A 206 VAL A 213 1 8 HELIX 15 15 GLY A 235 TYR A 246 1 12 HELIX 16 16 TYR A 246 ARG A 253 1 8 HELIX 17 17 PRO B 20 LEU B 31 1 12 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 TYR B 110 ASP B 112 5 3 HELIX 22 22 THR B 114 GLY B 123 1 10 HELIX 23 23 SER B 125 LYS B 133 1 9 HELIX 24 24 CYS B 144 VAL B 158 1 15 HELIX 25 25 ASP B 176 LEU B 187 1 12 HELIX 26 26 GLU B 192 ARG B 195 5 4 HELIX 27 27 SER B 203 ASN B 205 5 3 HELIX 28 28 ASP B 206 ALA B 212 1 7 HELIX 29 29 PRO B 234 LEU B 247 1 14 HELIX 30 30 LEU B 247 SER B 252 1 6
SHEET 1 AA 4 VAL A 35 PRO A 37 0 SHEET 2 AA 4 ILE A 2 THR A 5 1 O VAL A 3 N VAL A 36 SHEET 3 AA 4 ALA A 197 GLY A 201 1 O VAL A 198 N PHE A 4 SHEET 4 AA 4 LEU A 215 TYR A 218 1 O LEU A 215 N GLY A 199 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 THR A 140 0 SHEET 2 AC 3 TYR A 169 ALA A 172 -1 O ALA A 171 N GLU A 139 SHEET 3 AC 3 GLU A 161 HIS A 164 -1 O GLU A 161 N ALA A 172 SHEET 1 BA 4 VAL B 35 PRO B 37 0 SHEET 2 BA 4 ILE B 2 THR B 5 1 O VAL B 3 N VAL B 36 SHEET 3 BA 4 ALA B 197 GLY B 201 1 O VAL B 198 N PHE B 4 SHEET 4 BA 4 LEU B 215 TYR B 218 1 O LEU B 215 N GLY B 199 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 LYS B 77 -1 O ARG B 75 N VAL B 82 SHEET 1 BC 3 GLU B 139 THR B 140 0 SHEET 2 BC 3 TYR B 169 ALA B 172 -1 O ALA B 171 N GLU B 139 SHEET 3 BC 3 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 MG MG A1254 OD2 ASP A 6 1555 1555 2.22 LINK MG MG A1254 O ASP A 8 1555 1555 2.17 LINK MG MG A1254 O HOH A2004 1555 1555 2.31 LINK MG MG A1254 OD1 ASP A 202 1555 1555 2.32 LINK MG MG A1254 O HOH A2006 1555 1555 2.38 LINK MG MG A1254 O HOH A2007 1555 1555 2.35 LINK MG MG B1254 OD2 ASP B 6 1555 1555 2.18 LINK MG MG B1254 O HOH B2007 1555 1555 2.42 LINK MG MG B1254 O ASP B 8 1555 1555 2.30 LINK MG MG B1254 OD1 ASP B 202 1555 1555 2.35 LINK MG MG B1254 O HOH B2009 1555 1555 2.39 LINK MG MG B1254 O HOH B2006 1555 1555 2.38
CISPEP 1 PRO A 53 PRO A 54 0 6.16 CISPEP 2 PRO B 53 PRO B 54 0 4.98
SITE 1 AC1 7 ASP A 6 ASP A 8 ASP A 202 PO4 A1255 SITE 2 AC1 7 HOH A2004 HOH A2006 HOH A2007 SITE 1 AC2 10 ASP A 6 LEU A 7 ASP A 8 THR A 39 SITE 2 AC2 10 ALA A 40 LYS A 41 MG A1254 2M8 A1256 SITE 3 AC2 10 HOH A2004 HOH A2005 SITE 1 AC3 14 ASP A 8 LYS A 41 GLU A 45 TYR A 110 SITE 2 AC3 14 ARG A 135 THR A 140 GLY A 165 GLY A 166 SITE 3 AC3 14 ARG A 167 PHE A 168 HIS A 170 PO4 A1255 SITE 4 AC3 14 HOH A2004 HOH A2185 SITE 1 AC4 7 ASP B 6 ASP B 8 ASP B 202 PO4 B1255 SITE 2 AC4 7 HOH B2006 HOH B2007 HOH B2009 SITE 1 AC5 11 ASP B 6 LEU B 7 ASP B 8 THR B 39 SITE 2 AC5 11 ALA B 40 LYS B 41 MG B1254 2M8 B1256 SITE 3 AC5 11 HOH B2005 HOH B2006 HOH B2013 SITE 1 AC6 17 ALA B 40 LYS B 41 GLU B 45 TYR B 110 SITE 2 AC6 17 ARG B 135 THR B 140 GLY B 165 GLY B 166 SITE 3 AC6 17 ARG B 167 PHE B 168 HIS B 170 PO4 B1255 SITE 4 AC6 17 HOH B2006 HOH B2012 HOH B2013 HOH B2110 SITE 5 AC6 17 HOH B2135
CRYST1 39.368 88.049 146.457 90.00 90.00 90.00 P 21 21 21 8
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 0.025401 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011357 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006828 0.00000
MTRIX1 1 0.826970 -0.491910 0.272290 -0.35156 1
MTRIX2 1 -0.490210 -0.867990 -0.079280 -0.36389 1
MTRIX3 1 0.275340 -0.067920 -0.958940 0.23182 1