HEADER HYDROLASE 04-MAY-21 7MPD TITLE STRUCTURE OF SSOPTP BOUND TO 2-CHLOROETHYLSULFONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SSOPTP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_COMMON: SULFOLOBUS SOLFATARICUS; SOURCE 4 ORGANISM_TAXID: 2287; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN TYROSINE PHOSPHATASE, 2-CHLOROETHYLSUFLONATE, SSOPTP, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.PINKSTON,K.J.OLSEN,A.C.HENGGE,S.J.JOHNSON REVDAT 3 18-OCT-23 7MPD 1 REMARK REVDAT 2 06-OCT-21 7MPD 1 JRNL REVDAT 1 22-SEP-21 7MPD 0 JRNL AUTH J.PINKSTON,J.JO,K.J.OLSEN,D.COMER,C.A.GLAITTLI,J.P.LORIA, JRNL AUTH 2 S.J.JOHNSON,A.C.HENGGE JRNL TITL SIGNIFICANT LOOP MOTIONS IN THE SSOPTP PROTEIN TYROSINE JRNL TITL 2 PHOSPHATASE ALLOW FOR DUAL GENERAL ACID FUNCTIONALITY. JRNL REF BIOCHEMISTRY V. 60 2888 2021 JRNL REFN ISSN 0006-2960 JRNL PMID 34496202 JRNL DOI 10.1021/ACS.BIOCHEM.1C00365 REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 78770 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.530 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 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 36.5900 - 2.5300 1.00 5687 144 0.1499 0.1549 REMARK 3 2 2.5300 - 2.0100 1.00 5561 148 0.1328 0.1467 REMARK 3 3 2.0100 - 1.7500 1.00 5554 138 0.1223 0.1403 REMARK 3 4 1.7500 - 1.5900 1.00 5541 146 0.1048 0.1254 REMARK 3 5 1.5900 - 1.4800 1.00 5556 140 0.0926 0.1042 REMARK 3 6 1.4800 - 1.3900 1.00 5540 147 0.0941 0.1092 REMARK 3 7 1.3900 - 1.3200 1.00 5487 144 0.0931 0.1101 REMARK 3 8 1.3200 - 1.2600 1.00 5552 149 0.0947 0.1212 REMARK 3 9 1.2600 - 1.2200 1.00 5520 140 0.0913 0.1147 REMARK 3 10 1.2200 - 1.1700 1.00 5500 144 0.0946 0.1082 REMARK 3 11 1.1700 - 1.1400 1.00 5496 146 0.0962 0.1191 REMARK 3 12 1.1400 - 1.1000 1.00 5514 139 0.1100 0.1156 REMARK 3 13 1.1000 - 1.0800 0.98 5410 145 0.1344 0.1501 REMARK 3 14 1.0800 - 1.0500 0.88 4856 126 0.1738 0.1929 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.013 1445 REMARK 3 ANGLE : 1.234 1974 REMARK 3 CHIRALITY : 0.088 210 REMARK 3 PLANARITY : 0.008 250 REMARK 3 DIHEDRAL : 19.751 213 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 7MPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000255542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 84 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78794 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 17.00 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 0.66300 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: PHASER 2.8.0 REMARK 200 STARTING MODEL: 2I6I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 0.001 M ZINC CHLORIDE, 20% REMARK 280 PEG 6000, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.17600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 21.17600 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.17600 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 161 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 H ARG A 102 H101 ZLJ A 201 1.28 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 7 -8.27 72.39 REMARK 500 LYS A 7 -8.14 72.39 REMARK 500 CYS A 96 -140.76 -125.24 REMARK 500 VAL A 134 99.32 75.17 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 A 476 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A 477 DISTANCE = 7.17 ANGSTROMS REMARK 525 HOH A 478 DISTANCE = 7.60 ANGSTROMS REMARK 525 HOH A 479 DISTANCE = 7.63 ANGSTROMS REMARK 525 HOH A 480 DISTANCE = 7.70 ANGSTROMS REMARK 525 HOH A 481 DISTANCE = 7.94 ANGSTROMS REMARK 525 HOH A 482 DISTANCE = 8.39 ANGSTROMS REMARK 525 HOH A 483 DISTANCE = 9.13 ANGSTROMS REMARK 525 HOH A 484 DISTANCE = 11.43 ANGSTROMS REMARK 525 HOH A 485 DISTANCE = 14.25 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZLJ A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 202 DBREF 7MPD A 1 161 UNP Q97VZ7 Q97VZ7_SACS2 1 161 SEQRES 1 A 161 MET TYR TRP VAL ARG ARG LYS THR ILE GLY GLY SER GLY SEQRES 2 A 161 LEU PRO TYR THR GLU ASN GLU ILE LEU GLU TRP ARG LYS SEQRES 3 A 161 GLU GLY VAL LYS ARG VAL LEU VAL LEU PRO GLU ASP TRP SEQRES 4 A 161 GLU ILE GLU GLU SER TRP GLY ASP LYS ASP TYR TYR LEU SEQRES 5 A 161 SER ILE LEU LYS LYS ASN GLY LEU GLN PRO LEU HIS ILE SEQRES 6 A 161 PRO ILE PRO ASP GLY GLY VAL PRO SER ASP SER GLN PHE SEQRES 7 A 161 LEU THR ILE MET LYS TRP LEU LEU SER GLU LYS GLU GLY SEQRES 8 A 161 ASN LEU VAL HIS CYS VAL GLY GLY ILE GLY ARG THR GLY SEQRES 9 A 161 THR ILE LEU ALA SER TYR LEU ILE LEU THR GLU GLY LEU SEQRES 10 A 161 GLU VAL GLU SER ALA ILE ASP GLU VAL ARG LEU VAL ARG SEQRES 11 A 161 PRO GLY ALA VAL GLN THR TYR GLU GLN GLU MET PHE LEU SEQRES 12 A 161 LEU ARG VAL GLU GLY MET ARG LYS SER TRP LEU LYS ASN SEQRES 13 A 161 ILE TYR SER ASN SER HET ZLJ A 201 11 HET EPE A 202 32 HETNAM ZLJ 2-CHLOROETHANE-1-SULFONIC ACID HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 ZLJ C2 H5 CL O3 S FORMUL 3 EPE C8 H18 N2 O4 S FORMUL 4 HOH *185(H2 O) HELIX 1 AA1 THR A 17 GLY A 28 1 12 HELIX 2 AA2 GLU A 37 GLY A 46 1 10 HELIX 3 AA3 ASP A 47 ASN A 58 1 12 HELIX 4 AA4 SER A 74 GLU A 88 1 15 HELIX 5 AA5 ILE A 100 GLY A 116 1 17 HELIX 6 AA6 GLU A 118 LEU A 128 1 11 HELIX 7 AA7 THR A 136 MET A 149 1 14 HELIX 8 AA8 MET A 149 SER A 159 1 11 SHEET 1 AA1 5 TYR A 2 ARG A 5 0 SHEET 2 AA1 5 ILE A 9 SER A 12 -1 O GLY A 11 N TYR A 2 SHEET 3 AA1 5 ASN A 92 HIS A 95 1 O VAL A 94 N GLY A 10 SHEET 4 AA1 5 ARG A 31 VAL A 34 1 N LEU A 33 O LEU A 93 SHEET 5 AA1 5 GLN A 61 HIS A 64 1 O LEU A 63 N VAL A 34 SITE 1 AC1 12 GLY A 70 CYS A 96 VAL A 97 GLY A 98 SITE 2 AC1 12 GLY A 99 ILE A 100 GLY A 101 ARG A 102 SITE 3 AC1 12 GLN A 135 GLN A 139 HOH A 381 HOH A 431 SITE 1 AC2 6 THR A 17 GLU A 18 SER A 44 TYR A 158 SITE 2 AC2 6 HOH A 423 HOH A 441 CRYST1 83.923 83.923 42.352 90.00 90.00 120.00 P 63 6 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 0.011916 0.006880 0.000000 0.00000 SCALE2 0.000000 0.013759 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023612 0.00000