HEADER HYDROLASE 22-FEB-02 1L2P TITLE ATP SYNTHASE B SUBUNIT DIMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP SYNTHASE B CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DIMERIZATION DOMAIN (RESIDUES 62-122); COMPND 5 EC: 3.6.3.34; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: MM294; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PSD149 KEYWDS ALPHA HELIX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.A.DEL RIZZO,S.D.DUNN,Y.BI,B.H.SHILTON REVDAT 4 14-FEB-24 1L2P 1 REMARK REVDAT 3 31-JAN-18 1L2P 1 REMARK REVDAT 2 24-FEB-09 1L2P 1 VERSN REVDAT 1 05-JUN-02 1L2P 0 JRNL AUTH P.A.DEL RIZZO,Y.BI,S.D.DUNN,B.H.SHILTON JRNL TITL THE "SECOND STALK" OF ESCHERICHIA COLI ATP SYNTHASE: JRNL TITL 2 STRUCTURE OF THE ISOLATED DIMERIZATION DOMAIN. JRNL REF BIOCHEMISTRY V. 41 6875 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12022893 JRNL DOI 10.1021/BI025736I REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 682817.730 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 9325 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) : 0.282 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 972 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.65 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1295 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 147 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 494 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.81000 REMARK 3 B22 (A**2) : 3.43000 REMARK 3 B33 (A**2) : -9.24000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.15 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 13.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.630 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) : 1.360 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.900 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.360 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.500 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.43 REMARK 3 BSOL : 70.08 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.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1L2P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99203 REMARK 200 MONOCHROMATOR : HORIZONTALLY BENT SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9325 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.11700 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: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% ISOPROPANOL, 45% 2-METHYL-2,4 REMARK 280 -PENTANEDIOL, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 18.0K, TEMPERATURE 291.0K 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 17.85000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.85000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.38000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS A DIMER. REMARK 300 HOWEVER, THE BIOLOGICAL DIMER IS NOT CONTAINED IN THE CRYSTAL. REMARK 300 THE DIMER MODEL CANNOT BE GENERATED BY A SIMPLE COORDINATE REMARK 300 TRANSFORMATION OF THE CRYSTAL STRUCTURE. THE BIOLOGICAL DIMER REMARK 300 CAN, HOWEVER, BE MODELLED BASED ON THE SURFACE PROPERTIES OF REMARK 300 THE CRYSTAL STRUCTURE, AND ON SOLUTION SMALL-ANGLE X-RAY REMARK 300 SCATTERING DATA. 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 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 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 OD1 ASN A 80 OD1 ASN A 80 2555 2.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 1L2P A 62 122 UNP P0ABA0 ATPF_ECOLI 62 122 SEQRES 1 A 61 THR ASP GLN LEU LYS LYS ALA LYS ALA GLU ALA GLN VAL SEQRES 2 A 61 ILE ILE GLU GLN ALA ASN LYS ARG ARG SER GLN ILE LEU SEQRES 3 A 61 ASP GLU ALA LYS ALA GLU ALA GLU GLN GLU ARG THR LYS SEQRES 4 A 61 ILE VAL ALA GLN ALA GLN ALA GLU ILE GLU ALA GLU ARG SEQRES 5 A 61 LYS ARG ALA ARG GLU GLU LEU ARG LYS FORMUL 2 HOH *54(H2 O) HELIX 1 1 THR A 62 ARG A 121 1 60 CRYST1 35.700 40.760 42.350 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 0.028011 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023613 0.00000 TER 495 LYS A 122 HETATM 496 O HOH A 123 15.414 8.977 33.080 1.00 23.36 O HETATM 497 O HOH A 124 15.012 1.514 31.216 1.00 31.03 O HETATM 498 O HOH A 125 8.746 1.807 32.201 1.00 27.57 O HETATM 499 O HOH A 126 17.485 3.160 49.801 1.00 43.82 O HETATM 500 O HOH A 127 10.713 -0.641 30.456 1.00 36.04 O HETATM 501 O HOH A 128 0.189 2.316 7.079 1.00 33.72 O HETATM 502 O HOH A 129 1.967 5.100 -10.554 1.00 35.02 O HETATM 503 O HOH A 130 0.513 1.159 -9.086 1.00 28.13 O HETATM 504 O HOH A 131 10.522 8.448 17.531 1.00 38.28 O HETATM 505 O HOH A 132 1.550 8.626 -5.774 1.00 46.03 O HETATM 506 O HOH A 133 21.208 6.182 35.740 1.00 38.37 O HETATM 507 O HOH A 134 -0.625 4.957 -13.925 1.00 34.18 O HETATM 508 O HOH A 135 9.752 9.052 30.654 1.00 31.49 O HETATM 509 O HOH A 136 3.276 0.631 28.193 1.00 30.43 O HETATM 510 O HOH A 137 19.301 2.318 27.811 1.00 45.30 O HETATM 511 O HOH A 138 13.406 11.012 33.210 1.00 39.42 O HETATM 512 O HOH A 139 -3.632 4.308 2.637 1.00 39.44 O HETATM 513 O HOH A 140 -4.896 8.424 -17.755 1.00 38.80 O HETATM 514 O HOH A 141 14.323 9.585 40.386 1.00 44.36 O HETATM 515 O HOH A 142 12.854 7.968 46.513 1.00 36.75 O HETATM 516 O HOH A 143 11.104 1.826 48.199 1.00 46.13 O HETATM 517 O HOH A 144 2.823 3.884 24.670 1.00 45.44 O HETATM 518 O HOH A 145 -0.790 7.497 11.441 1.00 42.07 O HETATM 519 O HOH A 146 18.825 3.389 36.468 1.00 42.66 O HETATM 520 O HOH A 147 10.772 9.489 33.037 1.00 35.12 O HETATM 521 O HOH A 148 -6.902 0.958 -7.653 1.00 38.80 O HETATM 522 O HOH A 149 11.542 4.357 54.858 1.00 43.66 O HETATM 523 O HOH A 150 8.652 2.234 51.702 1.00 45.05 O HETATM 524 O HOH A 151 17.330 5.724 53.527 1.00 37.73 O HETATM 525 O HOH A 152 8.635 9.360 34.725 1.00 41.59 O HETATM 526 O HOH A 153 16.605 0.342 34.924 1.00 39.15 O HETATM 527 O HOH A 154 -5.924 11.857 -8.440 1.00 40.00 O HETATM 528 O HOH A 155 -0.603 2.226 9.873 1.00 44.73 O HETATM 529 O HOH A 156 11.358 5.467 52.621 1.00 41.08 O HETATM 530 O HOH A 157 6.789 3.948 5.986 1.00 38.84 O HETATM 531 O HOH A 158 -19.421 8.542 -28.900 1.00 39.03 O HETATM 532 O HOH A 159 17.772 1.315 30.789 1.00 34.49 O HETATM 533 O HOH A 160 11.907 9.847 19.370 1.00 44.56 O HETATM 534 O HOH A 161 8.873 1.358 35.037 1.00 44.47 O HETATM 535 O HOH A 162 4.118 10.697 14.970 1.00 42.70 O HETATM 536 O HOH A 163 -17.478 8.229 -22.154 1.00 45.34 O HETATM 537 O HOH A 164 3.554 5.015 -4.035 1.00 40.43 O HETATM 538 O HOH A 165 -8.364 3.245 -29.382 1.00 43.95 O HETATM 539 O HOH A 166 11.997 -2.874 30.855 1.00 34.38 O HETATM 540 O HOH A 167 14.113 9.655 45.410 1.00 38.77 O HETATM 541 O HOH A 168 19.822 6.580 42.785 1.00 34.90 O HETATM 542 O HOH A 169 -12.109 -1.226 -28.225 1.00 36.76 O HETATM 543 O HOH A 170 5.383 5.634 31.184 1.00 43.48 O HETATM 544 O HOH A 171 9.782 3.458 42.598 1.00 42.30 O HETATM 545 O HOH A 172 -0.131 7.394 14.102 1.00 41.64 O HETATM 546 O HOH A 173 -10.403 2.785 -35.727 1.00 40.47 O HETATM 547 O HOH A 174 -4.286 7.496 -21.435 1.00 40.93 O HETATM 548 O HOH A 175 8.882 8.209 38.970 1.00 37.32 O HETATM 549 O HOH A 176 15.552 -0.845 31.079 1.00 43.53 O MASTER 236 0 0 1 0 0 0 6 548 1 0 5 END