10 20 30 40 50 60 70 80 5F0Z - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 28-NOV-15 5F0Z
TITLE CRYSTAL STRUCTURE OF FRUCTOKINASE FROM VIBRIO CHOLERAE O395 IN TITLE 2 FRUCTOSE, ADP AND CALCIUM ION BOUND FORM
COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRUCTOKINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.1.4; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE SEROTYPE O1 (STRAIN ATCC 39541 SOURCE 3 / CLASSICAL OGAWA 395 / O395); SOURCE 4 ORGANISM_TAXID: 345073; SOURCE 5 STRAIN: ATCC 39541 / CLASSICAL OGAWA 395 / O395; SOURCE 6 GENE: CSCK, VC0395_0600; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET-28A+
KEYWDS KINASE, FRUCTOSE, ADP, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR R.PAUL,S.NATH,U.SEN
REVDAT 1 30-NOV-16 5F0Z 0
JRNL AUTH R.PAUL,S.NATH,U.SEN JRNL TITL CRYSTAL STRUCTURE OF FRUCTOKINASE FROM VIBRIO CHOLERAE O395 JRNL TITL 2 IN APO FORM JRNL REF TO BE PUBLISHED
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.PAUL,S.NATH,U.SEN REMARK 1 TITL CLONING, EXPRESSION, PURIFICATION, CRYSTALLIZATION AND REMARK 1 TITL 2 PRELIMINARY X-RAY ANALYSIS OF A FRUCTOKINASE FROM VIBRIO REMARK 1 TITL 3 CHOLERAE O395 REMARK 1 REF ACTA CRYSTALLOGR. SECT. F V. 68 1564 2015 REMARK 1 REF 2 STRUCT. BIOL. CRYST. COMMUN. REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 23192049 REMARK 1 DOI 10.1107/S1744309112047598
REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 29487 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1497 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 35.0075 - 3.8904 0.94 2601 124 0.1484 0.1510 REMARK 3 2 3.8904 - 3.0885 0.98 2583 123 0.1247 0.1858 REMARK 3 3 3.0885 - 2.6982 0.99 2557 143 0.1460 0.1966 REMARK 3 4 2.6982 - 2.4516 1.00 2540 141 0.1369 0.1676 REMARK 3 5 2.4516 - 2.2759 1.00 2566 147 0.1361 0.1734 REMARK 3 6 2.2759 - 2.1418 1.00 2536 128 0.1386 0.1759 REMARK 3 7 2.1418 - 2.0345 1.00 2554 129 0.1475 0.1870 REMARK 3 8 2.0345 - 1.9460 1.00 2501 139 0.1672 0.2321 REMARK 3 9 1.9460 - 1.8710 1.00 2528 143 0.1780 0.2219 REMARK 3 10 1.8710 - 1.8065 1.00 2511 144 0.1905 0.2302 REMARK 3 11 1.8065 - 1.7500 1.00 2513 136 0.2372 0.2746 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.330 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 : 0.012 2452 REMARK 3 ANGLE : 1.305 3357 REMARK 3 CHIRALITY : 0.077 379 REMARK 3 PLANARITY : 0.007 433 REMARK 3 DIHEDRAL : 14.958 865 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.5757 7.9612 -14.7950 REMARK 3 T TENSOR REMARK 3 T11: 0.0681 T22: 0.0108 REMARK 3 T33: 0.0140 T12: -0.0111 REMARK 3 T13: 0.0496 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 2.7665 L22: 2.2705 REMARK 3 L33: 2.6537 L12: 0.0173 REMARK 3 L13: 0.6923 L23: 0.0672 REMARK 3 S TENSOR REMARK 3 S11: -0.0882 S12: 0.0853 S13: -0.0566 REMARK 3 S21: -0.2001 S22: 0.0934 S23: -0.1086 REMARK 3 S31: 0.0729 S32: 0.0323 S33: 0.0904 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.1947 4.4151 -12.4818 REMARK 3 T TENSOR REMARK 3 T11: 0.0862 T22: 0.0488 REMARK 3 T33: 0.0640 T12: -0.0219 REMARK 3 T13: 0.0077 T23: -0.0106 REMARK 3 L TENSOR REMARK 3 L11: 1.5574 L22: 1.3302 REMARK 3 L33: 1.6101 L12: 0.6864 REMARK 3 L13: -0.5832 L23: -0.1192 REMARK 3 S TENSOR REMARK 3 S11: -0.0803 S12: 0.0430 S13: -0.1629 REMARK 3 S21: -0.0963 S22: 0.0188 S23: -0.0444 REMARK 3 S31: 0.1173 S32: -0.0192 S33: 0.0489 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 121 THROUGH 222 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.1561 17.7315 -1.0368 REMARK 3 T TENSOR REMARK 3 T11: 0.0614 T22: 0.0518 REMARK 3 T33: 0.0612 T12: -0.0102 REMARK 3 T13: -0.0061 T23: -0.0133 REMARK 3 L TENSOR REMARK 3 L11: 1.5272 L22: 1.3220 REMARK 3 L33: 0.9173 L12: 0.7454 REMARK 3 L13: -0.2714 L23: -0.2618 REMARK 3 S TENSOR REMARK 3 S11: 0.0304 S12: -0.0665 S13: 0.1254 REMARK 3 S21: 0.0747 S22: -0.0169 S23: 0.0414 REMARK 3 S31: -0.0409 S32: -0.0250 S33: -0.0021 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 223 THROUGH 323 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.5779 23.8199 -17.6317 REMARK 3 T TENSOR REMARK 3 T11: 0.1011 T22: 0.0933 REMARK 3 T33: 0.0789 T12: -0.0395 REMARK 3 T13: -0.0136 T23: 0.0234 REMARK 3 L TENSOR REMARK 3 L11: 1.1464 L22: 1.6694 REMARK 3 L33: 1.4351 L12: 0.5365 REMARK 3 L13: 0.4596 L23: 0.8396 REMARK 3 S TENSOR REMARK 3 S11: -0.1318 S12: 0.1310 S13: 0.1491 REMARK 3 S21: -0.1546 S22: 0.0884 S23: -0.0216 REMARK 3 S31: -0.1795 S32: 0.0882 S33: 0.0430 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 5F0Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215810.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30437 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.150 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.08 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 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: 1TZ6 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG 6000, 0.1M MES, PH 6.0, 3-4 REMARK 280 DAYS, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
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 53.44200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.13600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.44200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.13600 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: 4580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 787 LIES ON A SPECIAL POSITION.
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 MET A 1 REMARK 465 LYS A 2 REMARK 465 ALA A 3 REMARK 465 LEU A 4 REMARK 465 VAL A 5 REMARK 465 ARG A 6 REMARK 465 LEU A 7 REMARK 465 SER A 8 REMARK 465 SER A 9 REMARK 465 ASN A 10 REMARK 465 HIS A 11 REMARK 465 ILE A 12 REMARK 465 PHE A 13 REMARK 465 ARG A 14 REMARK 465 SER A 15
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 HE21 GLN A 187 O LEU A 210 1.55 REMARK 500 HH22 ARG A 192 O HOH A 510 1.57 REMARK 500 O HOH A 769 O HOH A 777 1.60 REMARK 500 O HOH A 800 O HOH A 827 1.82 REMARK 500 O3B ADP A 402 O HOH A 501 1.85 REMARK 500 OE2 GLU A 178 O HOH A 502 2.00 REMARK 500 O HOH A 520 O HOH A 818 2.09 REMARK 500 O HOH A 674 O HOH A 773 2.12 REMARK 500 O HOH A 558 O HOH A 732 2.13 REMARK 500 O HOH A 736 O HOH A 821 2.19 REMARK 500 OE2 GLU A 218 O HOH A 503 2.19 REMARK 500 O HOH A 596 O HOH A 791 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 807 O HOH A 839 2565 1.85 REMARK 500 O HOH A 538 O HOH A 811 1554 2.06 REMARK 500 O HOH A 736 O HOH A 760 1554 2.09 REMARK 500 O HOH A 819 O HOH A 839 2565 2.17 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 SER A 17 0.53 -63.50 REMARK 500 ASP A 34 85.55 -159.80 REMARK 500 SER A 58 21.57 80.18 REMARK 500 SER A 58 21.71 80.17 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 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 174 OD1 REMARK 620 2 HOH A 573 O 88.9 REMARK 620 3 HOH A 501 O 167.1 83.4 REMARK 620 4 HOH A 555 O 90.2 89.4 100.0 REMARK 620 5 HOH A 589 O 95.2 169.0 94.3 80.3 REMARK 620 6 HOH A 611 O 79.4 104.8 92.5 162.1 86.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 302 O REMARK 620 2 GLN A 305 O 100.3 REMARK 620 3 GLY A 307 O 155.2 101.8 REMARK 620 4 HOH A 546 O 91.2 96.0 97.6 REMARK 620 5 HOH A 661 O 72.0 131.2 84.9 131.4 REMARK 620 N 1 2 3 4
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FRU A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EY7 RELATED DB: PDB REMARK 900 5EY7 CONTAINS THE SAME PROTEIN IN APO FORM. REMARK 900 RELATED ID: 5EYN RELATED DB: PDB REMARK 900 5EYN COTAINS THE SAME PROTEIN IN FRUCTOSE, ADP, BEF3 BOUND FORM. REMARK 900 RELATED ID: 5F11 RELATED DB: PDB
DBREF1 5F0Z A 1 323 UNP A0A0H3AER7_VIBC3
DBREF2 5F0Z A A0A0H3AER7 1 323
SEQRES 1 A 323 MET LYS ALA LEU VAL ARG LEU SER SER ASN HIS ILE PHE SEQRES 2 A 323 ARG SER ASP SER MET SER ARG VAL TRP LEU THR GLY ASP SEQRES 3 A 323 ALA VAL VAL ASP LEU ILE PRO ASP GLY GLN GLN HIS TYR SEQRES 4 A 323 LEU LYS CYS PRO GLY GLY ALA PRO ALA ASN VAL ALA VAL SEQRES 5 A 323 ALA ILE ALA ARG LEU SER GLY ARG SER ALA PHE PHE GLY SEQRES 6 A 323 ARG VAL GLY ASN ASP PRO PHE GLY ARG PHE MET GLN GLN SEQRES 7 A 323 THR LEU THR ASP GLU GLN VAL ASP CYS GLN HIS LEU HIS SEQRES 8 A 323 PHE ASP PRO VAL HIS ARG THR SER THR VAL VAL VAL ASP SEQRES 9 A 323 LEU ASP GLU HIS GLY GLU ARG SER PHE THR PHE MET VAL SEQRES 10 A 323 LYS PRO SER ALA ASP GLN PHE LEU GLN LEU SER ASP ILE SEQRES 11 A 323 PRO SER PHE GLN LYS GLY GLU TRP LEU HIS VAL CYS SER SEQRES 12 A 323 ILE ALA LEU ALA ASN GLN PRO SER ARG SER SER THR PHE SEQRES 13 A 323 ALA ALA ILE ALA GLN MET LYS GLU VAL GLY GLY TYR VAL SEQRES 14 A 323 SER PHE ASP PRO ASN LEU ARG GLU GLU VAL TRP SER GLU SEQRES 15 A 323 PRO GLN GLU LEU GLN ALA THR VAL MET ARG ALA VAL GLY SEQRES 16 A 323 LEU ALA ASP VAL VAL LYS PHE SER GLU GLU GLU LEU GLN SEQRES 17 A 323 PHE LEU THR GLY THR GLN SER ILE GLU GLU GLY LEU GLN SEQRES 18 A 323 ALA ILE ALA ASP PHE GLN ILE PRO LEU VAL VAL VAL THR SEQRES 19 A 323 LEU GLY ALA LYS GLY ALA LEU VAL ALA THR PRO ASN SER SEQRES 20 A 323 GLN GLN ILE VAL SER GLY LYS ALA VAL LYS PRO ILE ASP SEQRES 21 A 323 THR THR GLY ALA GLY ASP ALA PHE VAL GLY GLY LEU LEU SEQRES 22 A 323 TYR ARG LEU SER VAL ALA GLN ASP TRP HIS ASN GLN ALA SEQRES 23 A 323 THR ILE LEU ASP ALA VAL LYS TRP ALA ASN GLY CYS GLY SEQRES 24 A 323 ALA LEU ALA THR THR GLN LYS GLY ALA MET THR ALA LEU SEQRES 25 A 323 PRO ASN GLN ALA ALA LEU TYR ALA PHE LEU GLU
HET FRU A 401 24 HET ADP A 402 39 HET CA A 403 1 HET NA A 404 1
HETNAM FRU FRUCTOSE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION
FORMUL 2 FRU C6 H12 O6 FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 CA CA 2+ FORMUL 5 NA NA 1+ FORMUL 6 HOH *350(H2 O)
HELIX 1 AA1 GLY A 45 LEU A 57 1 13 HELIX 2 AA2 ASP A 70 GLU A 83 1 14 HELIX 3 AA3 HIS A 108 ARG A 111 5 4 HELIX 4 AA4 SER A 120 LEU A 125 5 6 HELIX 5 AA5 GLN A 126 ILE A 130 5 5 HELIX 6 AA6 ILE A 144 ALA A 147 5 4 HELIX 7 AA7 PRO A 150 GLY A 166 1 17 HELIX 8 AA8 ARG A 176 TRP A 180 5 5 HELIX 9 AA9 GLU A 182 GLN A 184 5 3 HELIX 10 AB1 GLU A 185 GLY A 195 1 11 HELIX 11 AB2 GLU A 204 GLY A 212 1 9 HELIX 12 AB3 SER A 215 ILE A 223 1 9 HELIX 13 AB4 ALA A 224 GLN A 227 5 4 HELIX 14 AB5 GLY A 236 LYS A 238 5 3 HELIX 15 AB6 GLY A 263 ALA A 279 1 17 HELIX 16 AB7 ASN A 284 THR A 303 1 20 HELIX 17 AB8 ASN A 314 GLU A 323 1 10
SHEET 1 AA1 9 ASP A 86 ASP A 93 0 SHEET 2 AA1 9 SER A 61 GLY A 68 1 N VAL A 67 O ASP A 93 SHEET 3 AA1 9 VAL A 21 THR A 24 1 N LEU A 23 O ALA A 62 SHEET 4 AA1 9 TRP A 138 CYS A 142 1 O TRP A 138 N TRP A 22 SHEET 5 AA1 9 TYR A 168 ASP A 172 1 O SER A 170 N LEU A 139 SHEET 6 AA1 9 VAL A 199 SER A 203 1 O VAL A 199 N PHE A 171 SHEET 7 AA1 9 LEU A 230 THR A 234 1 O VAL A 232 N VAL A 200 SHEET 8 AA1 9 ALA A 240 THR A 244 -1 O ALA A 243 N VAL A 231 SHEET 9 AA1 9 SER A 247 VAL A 251 -1 O VAL A 251 N ALA A 240 SHEET 1 AA2 4 TYR A 39 GLY A 44 0 SHEET 2 AA2 4 VAL A 28 PRO A 33 -1 N ILE A 32 O LEU A 40 SHEET 3 AA2 4 SER A 99 VAL A 103 1 O VAL A 101 N LEU A 31 SHEET 4 AA2 4 PHE A 113 PHE A 115 -1 O THR A 114 N VAL A 102
LINK OD1 ASN A 174 CA CA A 403 1555 1555 2.27 LINK O ALA A 302 NA NA A 404 1555 1555 2.41 LINK O GLN A 305 NA NA A 404 1555 1555 2.43 LINK O GLY A 307 NA NA A 404 1555 1555 2.24 LINK CA CA A 403 O HOH A 573 1555 1555 2.39 LINK CA CA A 403 O HOH A 501 1555 1555 2.43 LINK CA CA A 403 O HOH A 555 1555 1555 2.39 LINK CA CA A 403 O HOH A 589 1555 1555 2.47 LINK CA CA A 403 O HOH A 611 1555 1555 2.41 LINK NA NA A 404 O HOH A 546 1555 1555 2.22 LINK NA NA A 404 O HOH A 661 1555 1555 2.38
CISPEP 1 LYS A 118 PRO A 119 0 -3.95 CISPEP 2 GLN A 149 PRO A 150 0 0.53
SITE 1 AC1 12 ASP A 26 ASP A 30 GLY A 45 ALA A 46 SITE 2 AC1 12 ASN A 49 VAL A 101 PHE A 113 PHE A 115 SITE 3 AC1 12 ARG A 176 ASP A 266 HOH A 573 HOH A 671 SITE 1 AC2 26 THR A 234 GLY A 236 GLY A 239 LYS A 254 SITE 2 AC2 26 ALA A 255 VAL A 256 PRO A 258 THR A 261 SITE 3 AC2 26 THR A 262 GLY A 263 ALA A 264 GLY A 265 SITE 4 AC2 26 PHE A 268 ASN A 296 GLY A 299 ALA A 300 SITE 5 AC2 26 CA A 403 HOH A 501 HOH A 504 HOH A 505 SITE 6 AC2 26 HOH A 514 HOH A 515 HOH A 530 HOH A 573 SITE 7 AC2 26 HOH A 674 HOH A 680 SITE 1 AC3 7 ASN A 174 ADP A 402 HOH A 501 HOH A 555 SITE 2 AC3 7 HOH A 573 HOH A 589 HOH A 611 SITE 1 AC4 5 ALA A 302 GLN A 305 GLY A 307 HOH A 546 SITE 2 AC4 5 HOH A 661
CRYST1 106.884 64.272 41.731 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 0.009356 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015559 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023963 0.00000