HEADER HYDROLASE 08-DEC-10 3PW9 TITLE STRUCTURAL AND FUNCTIONAL ANALYSIS OF ARABIDOPSIS THALIANA THYLAKOID TITLE 2 LUMEN PROTEIN ATTLP18.3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0603 PROTEIN AT1G54780, CHLOROPLASTIC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHOSPHATASE DOMAIN, UNP RESIDUES 84-235; COMPND 5 SYNONYM: ATTLP18.3, THYLAKOID LUMEN 18.3 KDA PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 STRAIN: CV. COLUMBIA; SOURCE 6 GENE: AT1G54780, T22H22.19; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX6P1 KEYWDS TAP DOMAIN, ROSSMANN FOLD, ACID PHOSPHATASE, PHOSPHOAMINO ACID KEYWDS 2 BINDING, THYLAKOID LUMEN MEMBRANE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.Y.WU,M.S.LIU,T.P.LIN,Y.S.CHENG REVDAT 3 01-NOV-23 3PW9 1 REMARK SEQADV LINK REVDAT 2 25-JAN-12 3PW9 1 JRNL REVDAT 1 26-OCT-11 3PW9 0 JRNL AUTH H.Y.WU,M.S.LIU,T.P.LIN,Y.S.CHENG JRNL TITL STRUCTURAL AND FUNCTIONAL ASSAYS OF ATTLP18.3 IDENTIFY ITS JRNL TITL 2 NOVEL ACID PHOSPHATASE ACTIVITY IN THYLAKOID LUMEN JRNL REF PLANT PHYSIOL. V. 157 1015 2011 JRNL REFN ISSN 0032-0889 JRNL PMID 21908686 JRNL DOI 10.1104/PP.111.184739 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 10387 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1068 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3550 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 131 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1174 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.72400 REMARK 3 B22 (A**2) : -8.92300 REMARK 3 B33 (A**2) : 8.19900 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.576 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.463 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.422 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.596 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 60.59 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : GOL.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : GOL.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PW9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062888. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-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 : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97622 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10968 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49600 REMARK 200 R SYM FOR SHELL (I) : 0.49600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3PVH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM ACETATE TRIHYDRATE, 0.1M REMARK 280 SODIUM CACODYLATE (PH 6.5), 25-30% (W/V) POLYETHYLENE GLYCOL REMARK 280 4000 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K 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 23.57350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.23200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.88100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.23200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.57350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.88100 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: 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 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 O HOH A 312 O HOH A 335 2.18 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 PRO A 157 13.53 -68.22 REMARK 500 GLU A 200 -83.67 -118.50 REMARK 500 LYS A 210 66.23 -113.03 REMARK 500 REMARK 500 REMARK: NULL 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 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 38 O REMARK 620 2 HOH A 39 O 88.2 REMARK 620 3 ASP A 103 OD2 101.9 121.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SER A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PTJ RELATED DB: PDB REMARK 900 RELATED ID: 3PVH RELATED DB: PDB DBREF 3PW9 A 84 235 UNP Q9ZVL6 U603_ARATH 84 235 SEQADV 3PW9 SER A 83 UNP Q9ZVL6 EXPRESSION TAG SEQRES 1 A 153 SER ALA SER GLU PHE ASN ILE LEU ASN ASP GLY PRO PRO SEQRES 2 A 153 LYS GLU THR TYR VAL VAL ASP ASP ALA GLY VAL LEU SER SEQRES 3 A 153 ARG VAL THR LYS SER ASP LEU LYS LYS LEU LEU SER ASP SEQRES 4 A 153 LEU GLU TYR ARG LYS LYS LEU ARG LEU ASN PHE ILE THR SEQRES 5 A 153 VAL ARG LYS LEU THR SER LYS ALA ASP ALA PHE GLU TYR SEQRES 6 A 153 ALA ASP GLN VAL LEU GLU LYS TRP TYR PRO SER ILE GLU SEQRES 7 A 153 GLU GLY ASN ASN LYS GLY ILE VAL VAL LEU ILE THR SER SEQRES 8 A 153 GLN LYS GLU GLY ALA ILE THR GLY GLY PRO ALA PHE ILE SEQRES 9 A 153 GLU ALA VAL GLY GLU ASN ILE LEU ASP ALA THR VAL SER SEQRES 10 A 153 GLU ASN LEU PRO VAL LEU ALA THR ASP GLU LYS TYR ASN SEQRES 11 A 153 GLU ALA VAL TYR SER SER ALA LYS ARG LEU VAL ALA ALA SEQRES 12 A 153 ILE ASP GLY GLN PRO ASP PRO GLY GLY PRO HET SER A 305 7 HET CA A 301 1 HET GOL A 302 6 HET GOL A 303 6 HETNAM SER SERINE HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SER C3 H7 N O3 FORMUL 3 CA CA 2+ FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 HOH *150(H2 O) HELIX 1 1 SER A 83 GLY A 93 1 11 HELIX 2 2 SER A 108 LYS A 127 1 20 HELIX 3 3 ASP A 143 TYR A 156 1 14 HELIX 4 4 SER A 158 ASN A 163 1 6 HELIX 5 5 GLY A 182 GLY A 190 1 9 HELIX 6 6 GLY A 190 GLU A 200 1 11 HELIX 7 7 GLU A 200 ASP A 208 1 9 HELIX 8 8 LYS A 210 ASP A 227 1 18 SHEET 1 A 4 VAL A 100 ASP A 102 0 SHEET 2 A 4 ARG A 129 VAL A 135 1 O THR A 134 N VAL A 101 SHEET 3 A 4 LYS A 165 ILE A 171 1 O VAL A 168 N ILE A 133 SHEET 4 A 4 GLU A 176 GLY A 181 -1 O GLU A 176 N ILE A 171 LINK O HOH A 38 CA CA A 301 1555 1555 3.02 LINK O HOH A 39 CA CA A 301 1555 1555 3.03 LINK OD2 ASP A 103 CA CA A 301 1555 1555 2.69 SITE 1 AC1 10 HOH A 32 HOH A 76 VAL A 100 VAL A 101 SITE 2 AC1 10 ASP A 102 LYS A 112 ASP A 208 LYS A 210 SITE 3 AC1 10 HOH A 326 HOH A 337 SITE 1 AC2 6 HOH A 38 HOH A 39 SER A 85 ASP A 103 SITE 2 AC2 6 ALA A 104 ARG A 136 SITE 1 AC3 7 HOH A 11 ASN A 88 THR A 111 ASP A 114 SITE 2 AC3 7 ASN A 212 GLU A 213 HOH A 332 SITE 1 AC4 3 PHE A 87 ASN A 91 LYS A 154 CRYST1 47.147 49.762 76.464 90.00 90.00 90.00 P 21 21 21 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 0.021210 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020096 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013078 0.00000